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Chapter 2

by: Nadezhda L Zakhariya

Chapter 2 CH 490 - 001

Nadezhda L Zakhariya
GPA 3.68

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About this Document

Goes over all the bonding, as well as properties of water, venturing into pH ad buffering. Lecture so far is very closely to the text, a section summary on Bicarbonate buffer mechanism (2.3) was i...
Steve L. Reichow
Class Notes
biochemistry, Lehninger Principles of Biochemistry, Biochemistry 1
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This 8 page Class Notes was uploaded by Nadezhda L Zakhariya on Sunday October 9, 2016. The Class Notes belongs to CH 490 - 001 at Portland State University taught by Steve L. Reichow in Summer 2016. Since its upload, it has received 6 views. For similar materials see BIOCHEM STRUCTURE & FUNCTION in Science at Portland State University.


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Date Created: 10/09/16
28.09.2016 Lecture Notes - ​ Ch. 2 - Water Weak interactions in an aqueous system Van der Waals, Ionic, dipole, Hydrogen bond interactions & influence on structure Van Der Waals (VdW (for simplicity)) - Weak interaction, universal, has attractive and repulsive properties (both of which are distance dependant.) Attractive Force:​ London Force -depends on polarizability Repulsive force:​ Steric repulsion -depends on size of atom, space it occupies Attraction V.S. repulsion Longer distance = ​attraction​ dominates Around .4-.7 nm (4 – 7 Angstroms (Å = 1/10 nm)) Short distance = ​repulsion There is an optimal distance for the VdW bond (VdW contact distance) Universal force field, happens between any two atoms that come close to each other EASILY broken, allows for reversal interactions - Small, but cumulatively in large molecules becomes a strong aspect that stabilizes the large structure IMPORTANCE? Sterics complementarity: How to molecules interact with each other, like proteins that need to fit like puzzle pieces Stabilizes biological macromolecules (ex: DNA, VdW stabilizes between nucleotide bases) Facilitates binding of polarizable ligands Hydrogen Bonding (H-Bond) - Electrostatic interaction between polar, uncharged molecules. 2​ves H​ O its properties, Helps with structure, important in binding substrate (lock & key), Base pairing of nucleic acids. Same as Dipole. Water serves as an ​H-DONOR​ (Acid) and H ​ -ACCEPTOR​ (base) Up to 4 H-bonds per molecule of H​ O 2​ H-Bonds (~20kJ/mole) Vs. (~420 kJ/mole) Weak! But strong compared to other bonds Gives water properties of: High bp, high mp, large surface tension -Typically involves ​two electronegative atoms​ ( often O & N) -​4-6KJ/mo​l for bonds w/neutral atoms. 6-10 kJ/mol w/ bonds with one charged atom. Bond energy dependant on the distance and steric restraints. - Strength dependant on ​distance and orientation. ​ Strongest = 3 atoms involved are in a line (O-H-O) Straight line stronger than at an angle. - How the bond is arranged will depend on the hybridization of the atom that the H is bonding with, as the location of lone pairs will be in a different position depending on hybridization. Physical properties of water Solvation, entropy, hydrophobic effect Water as a Solvent Works great for polar substances (amino acids, peptides, small alcohols, carbs, even polar gases), not so much for nonpolar (nonpolar gases, aromatic ​moieties​:(part or functional group of molecule), aliphatic chains.) ~Random Vocab: ​amphipathic​: having both polar and nonpolar particles on a molecule~ ​​ Why do salts dissolve in H O? 2 Dielectric constant - Reduces attraction between opp. Charged ions. At >40nm almost no attraction Strong electrostatic interactions - Between solvated ions and water, lowers energy of system ENTROPY - NaCl break into ions, entropy increase (less ordered) - Water has non random ordering as they began interacting with dissolved ions, entropy decreases Non polar gases are converted or bound to other molecules for transportation. Ex: CO​ +2​ater = Carbonic acid (HCO​ ) + Proton3​ Oxygen transportation via myoglobin and hemoglobin Hydrophobic effect - Minimizes losses of entropy in H​ O 2​ Why are hydrophobic molecules poorly dissolve in water? Entropyentropyentropy. Water → much disorder → much entropy Water + hydrophobic solute → more ordered → less entropy Low entropy → Thermodynamically unfavored → solubility of hydrophobic solute is low Hydrophobic effect Refers to the the folding of non-polar molecules in an aqueous solution. This effect is a main player behind: - Protein folding - Protein-protein interactions - Formations of micelles and membranes - Binding hormones (steroids) to receptors * * * Common misconception is that folding occurs due to some attraction between two non-polar molecules. THIS IS NOT THE CASE. In fact, when non-polar benzene is placed in water, ΔG<0 (favorable) but ΔH>0 (unfavorable). Origins of this effect: Water + amphipathic lipids → non-polar tails create ordered water → low entropy → unfavorable Increase entropy how? → place lipid molecules together, exchange some order for disorder. More and more lipid molecules come together, forming spherical structure called micelle (polar heads out, non-polar tails in), which created energetically favorable H-bonds with water. Water as a Ligand When structures are crystallized in a lab, only the ordered molecules can be seen in the x-ray. Using this technique, water molecules can be seen interacting in a specific order with these molecules, and show up in the x-ray. As they have a specific role and order, they should be considered as a ligand. It is the “21st” amino acid. ***Water plays an important role in maintaining structure and promoting function of proteins by acting as a ligand.*** Substrate and enzyme, water interacts with both, having a layer of ordered molecules around them. Bringing the two together releases some of the water molecules into the system, driving reaction entropically → favorable. Water and Osmotic Pressure - helps maintain homeostasis of cell Aquaporins regulate water entry and osmotic pressure. When a cell is placed in a hypotonic solution, creating large osmotic pressure and enters cell rapidly, bursting it (Not good) can lead to cell lysis. This process may also occur due to faulty water channels. Ionization of water and weak acid/base Gotthuss Mechanism, pH, pKa & Henderson Hasselbalch (HH) equation Water is also a reactant. - Ionization of water H​ O → H​ + HO​, left favored. Dissociation depends on temp. 2​ - Most water molecules remain undissociated (in H​ O form), and have2​ow electric conductivity - Want to conduct electricity → add salt → ions Equilibrium constant (K​ ): Conc. of reactants and products at equilibrium in M (mol/L) +​ -​ eq​ -16​ K​eq​H​ ][HO​]/[H​ O]2​ 1.8 x 10​ M @ 25°C H​ O D​ ensity: 1 g/ml @ 2 ​ 5​°C 2​ [H​2​] = 55.5 mol/L (M). can be determined from water density using molar mass Knowing this solving for [H​ ] or [HO​] becomes a cinch. +​ -​ K​eq​H​ ][HO​]/[H​ O] 2​ +​ -​ K​eq ​H​ O2​=[H​ ][HO​] ​ Larger K​ =a​tronger Acid = greater dissociation (large Ka) = smaller pKa (inverse relationship w/K​ a​ -pKa: easily express K​ a - pKa = -logK​ a -pKa ≠ pH. Changes from molecule to molecule Important numbers from lecture problems: -4 Lactic Acid Ka: 1.4 x 10​ Lactic Acid in blood is ~1mM After exercise, ~20mM Biological buffers and proton gradients Buffer​: mix of Weak Acid (WA) and Conjugate base (Weak base (WB)) that resists pH change - @ pH = pKa, 50:50 mix of WA and Conj. Base. BEST BUFFER CAPACITY - Buffering ability lost when pH different from pKa by 1 pH unit Many weak acid/base buffers in cell (most between 2-13 pKa) Determine pKa via titration. Can describe titration curve quantitatively via H ​ enderson-Hasselbalch eq. ​ -​ - pH = pKa + log [A​]/[HA] - [A​] = conj. Base M - [HA] = Weak Acid M - Useful for​: determining one of the components (pH/pKa/ratio of [A​]/[HA]) when given the rest of the information. WA/WB Important Concepts!! pH<pKa = WA/WB is protonated pH>pKa = WA/WB is deprotonated pH=pKa = WA/WB is 50:50 protonated/deprotonated These principles just like can be applied to common WA or WB, can be applied to amino acids and determine if they are protonated or deprotonated according to the pH. - amino acids have functional groups that are protonated/deprotonated at various pKa. - Ex: histidine - pKa​ 1​1.8 (carboxyl group) - pKa​ =6.0(imidazole group)(R group) 2​ - pKa​ 3​9.2(amino group) Biological buffer systems ● pH maintenance in cell is vital ​ - Blood plasma is buffered partly by the HCO​ and H​ CO​ , but is more complex than 3​ 2​ 3​ other buffer systems as H​ CO​ must also be 2​ equi3​brium with CO​ (a gas). 2​ +​ Lactic Acid → produces H​ → picked up by blood. - ​ +​ - HCO​ (in3​lood) + H​ (added) ⇋ H​ CO​ increases according2​o Le 3 ​telier's - Because H​ CO​ increases, so does dissolved (d) CO​ in blood because: 2​ 3​ 2 ​ - H​ CO​ ⇋ CO​ (d) + H​ O 2​ 3 ​ 2​ 2​ - As dissolved (d) CO​ increases, it2​hift the equilibrium with gaseous CO​ , raising its 2​ partial pressure in the lungs and leading to exhalation of extra CO​ 2 - CO​ (d2​⇋ CO​ (g) 2​ This mechanism occurs at the gain of H​ in the blood. At the loss of it, the reverse will occur, shifting the equilibrium of all the reactions to the left. The rate of respiration (inhaling/exhaling) easily adjusts these equilibriums, keeping the pH of blood nearly constant.


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