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Introduction II; Thermodynamics I

Introduction II; Thermodynamics I. Andy Howard Biochemistry Lectures, Spring 2019 17 January 2019, Illinois Tech. Water, catalysis, math, thermo. All of the above are critical to biochemistry; we’ll focus on those today. Water Catalysis Energy Regulation Molecular Biology Mathematics.

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Introduction II; Thermodynamics I

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  1. Introduction II; Thermodynamics I Andy Howard Biochemistry Lectures, Spring 201917 January 2019, Illinois Tech

  2. Water, catalysis, math, thermo All of the above are critical to biochemistry; we’ll focus on those today Intro 2; Thermo 1

  3. Water Catalysis Energy Regulation Molecular Biology Mathematics Thermodynamics Laws Realities Enthalpy and entropy Free energy Le Chatelier’s principle Protein folding Plans Intro 2; Thermo 1

  4. Water: a complex substance(CF&M Chapter 2) • Oxygen atom is covalently bonded to 2 hydrogens • Single bond character of these bonds means the H-O-H bond angle is close to 109.5º = acos(-1/3): actually more like 104.5º • This contrasts with O=C=O (angle=180º) or urea ((NH2)2-C=O) (angles=120º) • Two lone pairs available per oxygen:these are available as H-bond acceptors Intro 2; Thermo 1

  5. Water is polar (CF&M §2.1) • Charge is somewhat unequally shared • Small positive charge on H’s (d+); small negative charge on O (2d-) (Why?) • A water molecule will orient itself to align partial negative charge on one molecule close to partial positive charges on another. • Hydrogen bonds are involved in this. Intro 2; Thermo 1

  6. Liquid water is mobile • The hydrogen-bond networks created among water molecules change constantly on a sub-picosecond time scale • At any moment the H-bonds look like those in crystalline ice • Solutes disrupt the H-bond networks Intro 2; Thermo 1

  7. Water is a good solvent Polar molecules and ions are soluble in water Non-polar molecules aren’t Most, but not all, biologically important molecules are polar Intro 2; Thermo 1

  8. Water in reactions • Water is a medium wherein reactions occur; • But it also participates in reactions. • Enzymes often make water oxygen atoms better nucleophiles or water H’s better electrophiles • So water can participate in reactions that wouldn’t work without enzymes! Intro 2; Thermo 1

  9. Water’s physical properties • High heat capacity:stabilizes temperature in living things • High surface tension • Nearly incompressible (density almost independent of pressure) • Density max at 3.98ºC Intro 2; Thermo 1

  10. Catalysis • Catalysis is the lowering of activation energy barrier between reactants & products • How? • Physical surface on which reactants can be exposed to one another • Providing moieties that can temporarily participate in the reaction and be restored to their original state at the end Intro 2; Thermo 1

  11. Biological catalysts I • 1890’s: Emil Fischer realized that there had to be catalysts in biological systems • 1920’s: James Sumner said they were proteins • It took another 10 years forthe whole community to accept that Intro 2; Thermo 1

  12. Biological catalysts II • It’s now known that RNA can be catalytic too: • Can catalyze modifications in itself • Catalyzes the key step in protein synthesis in the ribosome • But we’ll mostly discuss proteinaceous enzymes in this course Intro 2; Thermo 1

  13. Energy in biological systems • We distinguish between thermodynamics and kinetics: • Thermodynamics characterizes the energy associated with equilibrium conditions in reactions • Kinetics describes the rate at which a reaction moves toward equilibrium Intro 2; Thermo 1

  14. Thermodynamics • Equilibrium constant is a measure of the ratio of product concentrations to reactant concentrations at equilibrium • Free energy is a measure of the available energy in the products and reactants • They’re related by DGo = -RT ln Keq Intro 2; Thermo 1

  15. Kinetics • Rate of reaction isdependent on Kelvintemperature T andon activation barrier DG‡ preventing conversion from one site to the other • Rate = Qexp(-DG‡/RT) = Qe-DG‡/RT • Job of an enzyme is to reduce DG‡ Svante Arrhenius Intro 2; Thermo 1

  16. What a catalyst accomplishes Temp, K Temp, K Intro 2; Thermo 1

  17. Regulation • Biological reactions are regulated in the sense that they’re catalyzed by enzymes, so the presence or absence of the enzyme determines whether the reaction will proceed • The enzymes themselves are subject to extensive regulation so that the right reactions occur in the right places and times Intro 2; Thermo 1

  18. Typical enzymatic regulation • Suppose enzymes are involved in converting A to B, B to C, C to D, and D to F. E is the enzyme that converts A to B: (E) A  B  C  D  F Intro 2; Thermo 1

  19. Regulation, continued In many instances F will inhibit (interfere) with the reaction that converts A to B by binding to a site on enzyme E so that it can’t convert A to B as readily. This feedback inhibition helps to prevent overproduction of F—homeostasis. Intro 2; Thermo 1

  20. Molecular biology • This phrase means something much more specific than biochemistry: • It’s the chemistry of replication, transcription, and translation, i.e., the ways that genes are reproduced and expressed. • Many of you have taken biology 214 or 515 or their equivalents; we’ll review some of the contents of those courses here, mostly near the middle of the semester. Intro 2; Thermo 1

  21. Molecules of molecular biology • Deoxyribonucleic acid: polymer; backbone is deoxyribose-phosphate; side chains are nitrogenous ring compounds • RNA: polymer; backbone is ribose-phosphate; side chains as above • Protein: polymer: backbone isNH-(CHR)-CO; side chains (R-groups) are 20 ribosomally encoded styles Intro 2; Thermo 1

  22. Steps in molecular biology:the Central Dogma • DNA replication (makes accurate copy of double-stranded DNA prior to mitosis) • Transcription (RNA version of DNA message is created) • Translation (mRNA copy of gene serves as template for making protein: 3 bases of RNA per amino acid of synthesized protein) Intro 2; Thermo 1

  23. How viruses can be so simple Viruses co-opt the replicative systems of their hosts, so they don’t need to carry around all the tools of their own synthesis Coding can be by RNA or DNA;RNA viruses code for a reverse transcriptase to make DNA from their RNA Intro 2; Thermo 1

  24. Evolution and Taxonomy • Traditional studies of interrelatedness of organisms focused on functional similarities • Enables production of phylogenetic trees • Molecular biology provides an alternative, possibly more quantitative, approach to phylogenetic tree-building • More rigorous hypothesis-testing possible Intro 2; Thermo 1

  25. Quantitation • Biochemistry is a quantitative science. • Results in biochemistry are significant only if they can be couched in quantifiable terms. • Thermodynamic & kinetic behavior of systems must be described quantitatively. • Even descriptive biochemistry, e.g. compartmentalization of reactions & metabolites into cells and organelles, must be characterized numerically. Intro 2; Thermo 1

  26. Mathematics in biochemistry • Ooo: I went into biology rather than physics because I don’t like math • Too bad. You need some math here:but not much. • Biggest problem in past years:exponentials and logarithms Intro 2; Thermo 1

  27. Exponentials • Many important biochemical equations are expressed in the form Y = ef(x) • … which can also be written Y = exp(f(x)) • The number e is the base of the natural logarithm system and is, very roughly, 2.718281828459045 • That is, it’s 2.7 1828 1828 45 90 45 Intro 2; Thermo 1

  28. Algebra of exponentials • Recognize that (eA)(eB) = e(A+B),or exp(A) exp(B) = exp(A+B) • Similarly eA/eB = e(A-B) • This becomes particularly useful when calculating ratios of similar quantities: • Arrhenius relationship says k = Qe-G‡/RT • Therefore: ratio of k values at two different temperatures is k1/k2 = e(G‡/R)(1/T2-1/T1) Intro 2; Thermo 1

  29. Logarithms • First developed as computationaltools: they convert multiplicationproblems into addition problems • They have a fundamental connection with raising a value to a power: • Y = xa logx(Y) = a • Thus Y = exp(a) = ea lnY = loge(Y) = a John Napier Intro 2; Thermo 1

  30. Algebra of logarithms • logv(A) = logu(A) / logu(v) • logu(A/B) = logu(A) - logu(B) • logu(AB) = Blogu(A) • log10(A) = ln(A) / ln(10)= ln(A) / 2.3026 = 0.4343 * ln(A) • ln(A) = log10(A) / log10e= log10(A) / 0.4343 = 2.3026 * log10(A) Intro 2; Thermo 1

  31. first: iClicker quiz, question 1! • 1. Which of the following statements is true? • (a) All enzymes are proteins. • (b) All proteins are enzymes. • (c) All viruses use RNA as their transmittable genetic material. • (d) None of the above. Thermodynamics

  32. iClicker quiz, question 2 • 2. Biopolymers are generally produced in reactions in which building blocks are added head to tail. Apart from the polymer, what is the most common product of these reactions?(a) Water (b) Ammonia(c) Carbon Dioxide (d) Glucose(e) None of the above. Polymerization doesn’t produce secondary products Thermodynamics

  33. iClicker quiz, question 3 • 3. Which type of biopolymer is sometimes branched?(a) DNA(b) Protein(c) Polysaccharide(d) RNA(e) They’re all branched. Thermodynamics

  34. iClicker quiz, concluded Free Energy G • 4. The red curve represents the reaction pathway for an uncatalyzed reaction. Which one is the pathway for a catalyzed reaction? A D B C Reaction Coordinate Thermodynamics

  35. Thermodynamics! • CF&M §1.6 • Moran et al. (textbook we used previously in this course) put this subject in the middle of chapter 10;Other textbooks, including ours, are smart enough to put it in the beginning. • You can tell which I prefer! Intro 2; Thermo 1

  36. Why we care G ReactionCoordinate • Free energy is directly related to the equilibrium of a reaction • It doesn’t tell us how fast the system will come to equilibrium • Kinetics, and the way that enzymes influence kinetics, tell us about rates • Today we’ll focus on equilibrium energetics; we’ll call that thermodynamics Intro 2; Thermo 1

  37. Laws of Thermodynamics • Traditionally four (0, 1, 2, 3) • Can be articulated in various ways • First law: The energy of an isolated system is constant. • Second law: Entropy of an isolated system increases. Intro 2; Thermo 1

  38. What do we mean by systems, closed, open, and isolated? • A system is the portion of the universe with which we’re concerned (e.g., an organism or a rock or an ecosystem) • If it doesn’t exchange energy or matter with the outside, it’s isolated. • If it exchanges energy but not matter, it’s closed • If it exchanges energy & matter, it’s open Intro 2; Thermo 1

  39. That makes sense if… • It makes senseprovided that we understand the words! • Energy. Hmm. Capacity to do work. • Entropy: Disorder. (Boltzmann): S = kBlnW • Isolated system: one in which energy and matter don’t enter or leave • An organism is not an isolated system:so S can decrease within an organism! Boltzmann Gibbs Intro 2; Thermo 1

  40. Thermodynamic properties • Extensive properties:Thermodynamic properties that are directly related to the amount (e.g. mass, or # moles) of stuff present (e.g. E, H, S) • Intensive properties: not directly related to mass (e.g. P, T) • If you divide an extensive property by mass or # of moles, you get an intensive property Intro 2; Thermo 1

  41. Units • Energy unit: Joule (kg m2 s-2) • 1 kJ/mol = 103J/(6.022*1023)= 1.661*10-21 J • 1 cal = 4.184 J:so 1 kcal/mol = 6.948 *10-21 J • 1 eV = 1 e * J/Coulomb =1.602*10-19 C * 1 J/C = 1.602*10-19 J= 96.4 kJ/mol = 23.1 kcal/mol James Prescott Joule Intro 2; Thermo 1

  42. Typical energies in biochemistry • Go for hydrolysis of high-energy phosphate bond in adenosine triphosphate:33kJ/mol = 7.9kcal/mol = 0.34 eV • Hydrogen bond: 4 kJ/mol=1 kcal/mol • van der Waals force: ~ 1 kJ/mol • See textbook for others Intro 2; Thermo 1

  43. Enthalpy, H • Closely related to energy:H = E + PV • Therefore changes in H are:H = E + PV + VP • Most, but not all, biochemical systems have constant V, P: H = E • Related to the heat content in a system Kamerlingh Onnes Intro 2; Thermo 1

  44. Entropy, S • Related to disorder: Boltzmann: S = k ln kB=Boltzmann constant = 1.38*10-23 J K-1 • Note that kB = R / N0 •  is # of degrees of freedom in the system • Entropy in 1 mole = N0S = Rln • Number of degrees of freedom can be calculated for simple molecules Intro 2; Thermo 1

  45. Components of entropy Liquid propane (as surrogate): Intro 2; Thermo 1

  46. Real biomolecules • Entropy is mostly translational & rotational • Enthalpy is mostly electronic • Translational entropy = (3/2) R ln Mr • So when a molecule dimerizes, the total translational entropy decreases(there’s half as many molecules,but ln Mr only goes up by ln 2) • Rigidity decreases entropy Intro 2; Thermo 1

  47. Entropy in solvation: solute • When molecules go into solution, their entropy increases because they’re freer to move around Intro 2; Thermo 1

  48. Entropy in solvation: Solvent • Solvent entropy usually decreases because solvent molecules must become more ordered around solute • Overall effect: typically slightly tending toward solution Intro 2; Thermo 1

  49. Entropy matters a lot! • Most biochemical reactions involve small ( < 10 kJ/mol) changes in enthalpy • Driving force is often entropic • Increases in solute entropy often is at war with decreases in solvent entropy. • The winner tends to take the prize. Intro 2; Thermo 1

  50. Apolar molecules in water • Water molecules tend to form ordered structure surrounding apolar molecule • Entropy decreases because they’re so ordered Intro 2; Thermo 1

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