bch 5045 graduate survey of biochemistry - environmental...
TRANSCRIPT
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BCH 5045
Graduate Survey of Biochemistry
Instructor: Charles GuyProducer: Ron ThomasDirector: Glen Graham
Lecture 5Slide sets available at:
http://hort.ifas.ufl.edu/teach/guyweb/bch5045/index.html
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• LEHNINGER• PRINCIPLES OF BIOCHEMISTRY
• Fifth Edition
David L. Nelson and Michael M. Cox
© 2008 W. H. Freeman and Company
CHAPTER 13Bioenergetics and Biochemical
Reaction Types
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Gibbs equation
∆G = ∆H – T∆S
Define free-energy, G; entropy, S and H, enthalpy
For A + B C + D, then
Keq = [C][D]/[A][B], thus
∆G = ∆G° + RTln[C][D]/[A][B] or ∆G° = -RTlnKeq
State the 1st and 2nd
Laws of Thermodynamics
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The chemistry of ATP and other nucleoside triphosphates is key and centrally important to their function and tightly related to the nature of the phosphoanhydridebond between the phosphate groups.
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Requires energy input Can provide energy A coupled reaction that is energetically favorable with a product that can provide an accessible store of energy
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Typical model reaction free energy transformation coordinate
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A stylized depiction of the flow of energy in humans. The ultimate source of the energy we need and use is from the sun and was transformed into chemical forms by photosynthetic organisms. The catabolic processes provide chemical forms of energy to be consumed in anabolic processes.
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Chemical forms that have bond structures that are energy enriched and in which can be made available to do work.
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This table shows the inextricable linkage between Keq and standard free energy of chemical reactions. Both indicate how far a reaction will proceed to reach equilibrium.
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High energy content metabolites central to cellular function. All contain phosphorus, even CoA.
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ATP and nucleoside triphosphates are versatile and offer three high energy linkages that can be exploited in chemical reactions.
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Reactions with strongly negative ΔG´° values.
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What is free energy and why is this important?
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What is going on here?
ATP
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• LEHNINGER• PRINCIPLES OF BIOCHEMISTRY
• Fifth Edition
David L. Nelson and Michael M. Cox
© 2008 W. H. Freeman and Company
CHAPTER 2
The Foundations of Biochemistry
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WaterWater is pure, Water is natural, Water is healthy, Water can help all
Water is simple, Water is free, Water can help the lives, The lives of you and me
Olivia Taylor
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Water is the solvent of life
It is required for the function of all active cells and biological entities associated with cells. The properties of water are so very extremely profound in their biological significance. The ultimate structure and shape of many of the compounds on which life is based, proteins, nucleic acids, lipids, and carbohydrates result from their direct interaction with water.
The physical properties of water are so unusual relative to other compounds of similar composition and size that it is reasonable to assume that where there is no water there can be no life.
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Water is present in high concentration (~55.6 M), its shape is triangular, and it has a polar character. Having polarity means that one side of the molecule is charged differently than the opposite side. The asymmetrical charge distribution in water is caused by the propensity of the oxygen nucleus to draw the electrons shared with the two hydrogen atoms closer to it and away from the hydrogen.
A polar compound is said to be a dipole. Water is a dipole of 1.84 debye units or a dielectric constant of 80.2 at 20°C (1 debye = 0.21 Å in charge separation).
The highly polar nature of water makes it an extremely good solvent for compounds with polar character.
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In fact, as the dielectric constant of a medium increases its ability to keep opposite charged molecules apart increases according to Coulomb's Law
1. F = kq1q2Dr2
where F is the force between electrical charges, q1 and q2 separated by a distance r. D is the dielectric constant of the medium (solvent) and k is the proportionality constant (8.99 X 109).
The high dielectric constant of water means that the force between two electrical charges will be reduced.
Thus NaCl readily dissolves in water.
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Water molecules can interact with charged components of compounds forming hydration shells that neutralize charge and helps to keep oppositely charged atoms from coalescing into an insoluble salt.
Many of the compounds that make up cells are polar, but some are nonpolar. These compounds do not mix well or dissolve in water. An example of this is the mixing or nonmixing of oil with water (the salad dressing dilemma). In this case, the theme is "like dissolves like."
This leads to an important paradigm of hydrophilic and hydrophobic interactions in biochemical structure and function.
Nonpolar compounds in an aqueous environment tend to associate together excluding water from the interior of the conglomeration and this is called hydrophobic attraction.
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In the case of a fatty acid suspended in water, micelle formation will occur. In reality, there is no actual attraction between nonpolar molecules that causes them to associate in this manner.
When a nonpolar compound is surrounded by water the normal positioning of the water molecules in the vicinity of that compound is disrupted. This disruption of the normal positioning and free movement of water molecules leads to the formation of an ordered arrangement of a large number of water molecules into a cage like structure. Such structures are called clathrates. Highly ordered clathrate structures are energetically not favored.
The coalescence of individual nonpolar molecules together is more energetically favorable. Consequently, the energy of the system is minimized as the nonpolar molecules coalesce out of contact with water.
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Given the polarity of the water molecule, electrons are unequally distributed and this gives rise to an attraction between a hydrogen atom of one water molecule with the electrons of an oxygen atom of another water molecule.
Bond angles of water are similar to those expected of a tetrahedral and suggest that the polar nature of the orbitals is equivalent to sp3 hybrids.
Water is not linear. The two hydrogen atoms occupy the corners of the tetrahedron and the nonbonding pairs of oxygen’s electrons occupy the other corners.
The electron orbital structure of the oxygen in a water molecule is such that two hydrogen atoms from two different water molecules can interact with the oxygen of another water molecule.
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This linear attraction between the oxygen and the hydrogen atoms of different water molecules is none other than a hydrogen bond (H-bond). Actually, the hydrogen atom can form a H-bond with an N or O atom that is weakly basic and can act as an acceptor. This is made possible by the hydrogen atom's small size, which permits it to approach a lone-pair electron cloud of acceptor atoms.
The nucleus of H is the only one small enough to approach within the van der Waals distance and get close enough for an electrostatic interaction to exist.
The H-bond distance of water is about 0.18 nm.
Please view this video: http://www.youtube.com/watch?v=LGwyBeuVjhU&feature=related
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This capacity to form H-bonds gives water its uncommon physical properties. Although weak compared to covalent bonds (20 kj/mol vs ca 150-500 kj/mol), the enormous number of H-bonds (4-5 kcal/mol; 1 cal = 4.18 joules) that exist at any given moment in water are central to its physical properties.
The turnover rate of a H-bond in water is extremely rapid at 10-11/sec.
Each water molecule can form as many as four H-bonds.
Liquid water possesses about 85% of the maximal H-bonds possible. In contrast, ice contains roughly 99% of the possible H-bonds.
Hydrogen bonding makes liquid water molecules extremely cohesive.
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The constant translational and rotational movements of water molecules in solution are surprisingly not as well understood as one may assume, yet are believed to underlie water’s unique physical properties and its central role in biological systems.
Our understanding of bulk water’s structure and dynamics despite intensive study remains limited.
Recent experimental advances are helping to reveal the “dance” of water molecular dynamics when interacting with simple molecules and ions.
Some of the latest experiments use "ultrashort" infrared pulses with durations on the order of 50 x 10–15 s, or 50 fs. By using such short pulses it becomes possible to resolve some of the elementary “dance” steps.
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An infrared frequency is chosen to excite stretching vibrations of the OH bonds.
The vibrational frequency of the OH group shifts when the H atom changes its hydrogen-bond environment. The ultrashort infrared pulses can be used to measure time-dependent fluctuations in the vibrational frequency in a process called "spectral diffusion," where therotational dynamics of the OH bond is measured by using polarized light.
In one example, it has been shown that a water molecule shifts its donated H-bonds betweenwater and perchlorate (anion) acceptors by a large, angular rotation of 49 ± 4°. http://www.youtube.com/watch?v=D3mbOzOYzQ0
As we better understand water’s unique molecular properties, we will better understand why it is the solvent of life.
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The unusual physical properties of water include:
a high surface tension relative to NH3, creating a high cohesiveness. This cohesiveness is so important to plants because it permits the capillary movement of water from the roots to the canopy. Without the high cohesiveness of water, trees and certainly trees like the Redwoods could not exist;
a high viscosity;
a high heat capacity 1 cal/g/°C between 14.5° and 15.5°C; a high boiling point; otherwise would boil at -100°C without H-bonds;
Physical Property H2O NH3 CH4 H2S Molecular Weight 18 17 16 34 Boiling Point (C) 100 -33 -161 -61
Freezing Point (C) 0 -78 -183 -86 Viscosity (centipoise) 1.01 0.25 0.10 0.15
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a high heat of fusion 80 cal/g or 6 kj/mol which decreases the H-bonds from 99% down to 85%;
and a high heat of vaporization 540 cal/g or 41 kj/mol which decreases H-bonds from 85% down to near 0%. This is significant because vaporization consumes much heat and provides significant cooling capacity.
Water can act as a Bronsted-Lowry acid:
H2O + NH3 ↔ OH‾ + NH4+
acid base base acid
or as a base:
H2O + HCO3‾ ↔ H3O+ + CO32-
base acid acid base
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However, absolutely pure water has a neutral pH! So, what is the pH of water that has reached equilibrium with the ambient atmosphere?
Why is this becoming an increasingly worrisome problem?
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• LEHNINGER• PRINCIPLES OF BIOCHEMISTRY
• Fifth Edition
David L. Nelson and Michael M. Cox
© 2008 W. H. Freeman and Company
CHAPTER 2
The Foundations of Biochemistry
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Figure 2-1 Structure of the water molecule
Page
39
From Biochemistryby Voet & Voet, Third edition, 2004
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Figure 2-2 Hydrogen bond between two water molecules.
Page
40
From Biochemistryby Voet & Voet, Third edition, 2004
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Figure 2-3 Structure of ice.
Page
40
From Biochemistryby Voet & Voet, Third edition, 2004
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Figure 2-5 Solvation of ions by oriented water molecules.
Page
42
From Biochemistry by Voet & Voet, Third edition, 2004
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Water is not like any of the other compounds listed above. It has a high melting point, a high boiling point and a high heat of vaporization.
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The water cages are know as clathrates, and because they are highly ordered, they represent one form of energy described in the Gibbs equation.
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The following slides are included but were not shown in the lecture 5 video.
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Diagram of the structure of ice.
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Hydrogen bonding
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Note: What does amphipathic mean?
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Polar molecules are hydrophilic, meaning they love water, and in the case shown here water can dissociate the Na and Cl from the crystal lattice.
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