1 / 16

Cross References with Lunine Textbook

Cross References with Lunine Textbook. Have done: Background on Biomolecules – see 4.1-4.3 Prebiotic chemistry and RNA World – see 9.4-9.5 Replicators v. Autocatalysis – see 9.1-9.3 Will do: Thermodynamics – see 7.4-7.5

griffith-newton
Download Presentation

Cross References with Lunine Textbook

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Cross References with Lunine Textbook Have done: Background on Biomolecules – see 4.1-4.3 Prebiotic chemistry and RNA World – see 9.4-9.5 Replicators v. Autocatalysis – see 9.1-9.3 Will do: Thermodynamics – see 7.4-7.5 Metabolism, Respiration, Photosynthesis – see 4.6-4.7 (also Molecular Biology of the Cell, Alberts et al.) Extremophiles – see Chap 10

  2. Energy in Cells Aims – Thermodynamics of molecular interactions and chemical reactions. How do cells get their energy? Metabolism. Respiration. Photosynthesis. How did these processes evolve? How did the first organisms get their energy? Cyanobacteria Anabaenopsis a bloom of cyanobacteria

  3. But before we get to all that, we need to understand the dreaded topic of Thermodynamics Gibbs Free Energy: G = H - TS H is enthalpy – equivalent to heat energy – can be stored in physical interactions between molecules and in chemical bonds. S is entropy – measure of randomness or disorder – how many configurations are accessible to the molecules. Technicality: H = E + PV (heat input at constant pressure) Spontaneous reaction: G < 0 if G > 0, reaction requires energy input. At equilibrium G = 0 Think about ice/water

  4. G C }DG = -3.0 kcal/mol G C }DG = -2.1 kcal/mol U A }DG = -1.2 kcal/mol U A loopDG = + 4.5 kcal/mol C U C U Example of RNA folding Thermodynamics parameters are measured on real molecules. Helix formation = hydrogen bonds + stacking Entropic penalty for loop formation. Total G = - 1.8 kcal/mol 1 kcal = 4.184 kJ (specific heat capacity of water) G = - 7.53 kJ/mol This loop is stable at this temperature. Will melt at higher temp. Stability is sequence specific.

  5. Chemical potential = change in G when a molecule is added to a solution concentration of molecule X in moles/litre (M) standard chem pot in 1M solution gas constant R = 8.314 J K-1 mol-1 absolute temperature in K The concentration term comes from treating a solution like an ideal gas

  6. Gfold = -7.53 kJ/mol unfolded folded Temp T = 273 + 37 = 310K At equilibrium Gtot = 0. Therefore: [Xfold]/[Xun] = exp(+ (7.53 × 1000) /(8.314 × 310)) = exp(2.92) = 18.5

  7. For charged molecules need to add potential term. Faraday = charge per mole of electrons no. of charges on ion Membranes Permeable to water and some small molecules. Not permeable to large molecules. Not permeable to ions (because of hydrophobic interior of membrane). [Xout] [Xin] For concentration ratio of 100, Gmemb =8.314 × 310 × ln(100) = 12 kJ/mol Molecules will not spontaneously go up a concentration gradient. G0 of hydrolysis of ATP = -30.5 kJ/mol. Hydrolysis of 1 mole of ATP is more than enough to drive transport of 1 mole of X against the concentration gradient.

  8. Simple diffusion is passive – down the concentration gradient A passive channel is a catalyst – speeds up reaction but does not change equilibrium Carrier mediated – one molecule goes downhill whilst the other goes up. Sum of two is downhill. Active transport – use chemical energy to pump a molecule uphill.

  9. Free energy of chemical reactions similarly for B, C, and D nAA + nBB  nCC + nDD Free energy change of reaction under standard conditions of 1 M concentration of each species. where At equilibrium G = 0. Therefore Define the equilibrium constant as Therefore at equilibrium

  10. example: ATP hydrolysis ATP4- + H2O  ADP3- + H+ + HPO42- G0 = -30.5 kJ/mol. Therefore, K = exp(30.5 x 1000/8.314 x 310) = 1.38 x 105 This is large: there would be much more ADP than ATP at equilibrium. The cell is not at standard 1 M conc of all molecules. The free energy available from ATP hydrolysis depends on the concentrations – estimated between -25 and -40 kJ/mol. Energy input from metabolism can drive the reaction in reverse. Keeps ATP conc high. The Cell is Not at Equilibrium Cell is in a non-equilibrium steady state governed by balance of input and dissipation of energy and balance of input of food molecules and output of waste.

  11. Oxidation of reduced carbon compounds releases energy (gas/oil/food) Need to control this. An explosion in the gas tank does not make the car go far. See also fig 4.22 of Lunine When Greaction < 0 for a reaction, this energy can in principle be used to form molecules for which Gformation > 0. However – nothing is 100% efficient. Always get dissipation of energy as heat.

  12. effect of catalyst Activation energy and catalysts A + B  C + D Gact forward reaction rate = k[A][B]exp (-(G0r + Gact)/RT) backward reaction rate = k[C][D]exp(-Gact/RT) C+D G0r A+B At equilibrium, forward and backward rates are equal. Therefore The equilibrium constant does not depend on the activation energy. A catalyst lowers the activation energy by binding to the transition state. Speeds up both forward and backward reactions. It can make you go uphill faster but it doesn’t keep you there...

  13. Catalyzing some reactions can drive a particular pathway. Results in specific products not equilibrium distribution of products.

  14. Oxidation – adding oxygen Reduction – adding hydrogen Oxidation – removing electrons Reduction – adding electrons H H H H | | \ \ H-C-H H-C-OH C=O C=O O=C=O | | / / H H H HO + + 2- 2- 4- 0 + + 2- 4+ + + Methane Methanol Formaldehyde Formic acid Carbon dioxide Fe2+ Fe3+ + e- C is more electronegative than H – in methane C is slightly negative O is more electronegative than C – in carbon dioxide, C is slightly positive Oxidation removes electrons from C.

  15. Oxidation Reduction H2S S0 S2O32- SO32- SO42- NH4+ N2 NO2- NO3- Hydrogen Elemental Thiosulphate Sulphite Sulphate sulphide sulphur Ammonium Nitrogen Nitrite Nitrate gas Redox reactions – always one thing reduced and one thing oxidized. (Redox reactions drive chemosynthesis – see next section on chemoautotrophs) Ared + Box Aox + Bred symbolizes electron transfer. (Redox reactions occur in electron transport chains. See next section on respiration and photosynthesis)

  16. Nicotinamide adenine dinuclotide NAD+ oxidizing agent (electron acceptor) Adenosine triphosphate (ATP) also transfers phosphate group NADH reducing agent (electron donor) Acetyl coenzyme A (Acetyl CoA) also transfers carbons Activated carrier molecules = energy currency All these molecules have nucleotide ‘handles’ with which they interact with enzymes. Probably used to interact with ribozymes. More evidence for the RNA world. NAD+ + H+ + 2e-  NADH Half a reaction: the electron goes somewhere.....

More Related