L2, L3 water and weak interactions

L2, L3 water and weak interactions Why do we care about water? - Cells have a high portion of water - Water participates in a lot of reactions - Water is the medium for life as it protects from UV. - Reactions occur in an aqueous medium The interaction with Water is essential to allow functions eg for proteins ATP is formed by a condensation reaction between ADP and phosphatase, this reaction requires energy. The hydrolysis of ATP to form ADP + P releases an equivalent amount of energy. Water bound to protein is essential to its function. - Weak interactions in aqueous systems - Hydrogen bonds Ionic interactions Hydrophobic interactions Van der waals interactions Hydrogen bonds: - Water: polar → NOT an ION, oxygen high electronegativity (H has 1 electron each), h bonds, covalent bonds between the O and 2 H - - Usually, H bonds are with two electronegative atoms (mostly N or O)→ stron dipolediplole or charge-dipole interaction o There is a Hydrogen donor- the one who is connected to it → ACID o There is a hydrogen acceptor, the one with the eg O that is attracted to the other H → BASE In 1 water molecule the max. number of Hydrogen bonds that can be made is 4 o Highest number is seen in ice (Hexagonal ice: more H-bonds → lower density→ floats) o H- bonds of water are cooperative o In water approx 3.5 H Bonds - Depending on the shape of the H bond, it is stronger or weaker. If it’s in line, its stronger, if it’s bent its weaker (strongest weak interaction) - They’re super important because: o Structure and function of proteins, DNA, polysaccharides o Binding of substrates to enzymes and of hormones to receptors o Matching mRNA and tRNA Weak interaction, but participates in pretty much everything Ionic Interactions: - Electrostatic interactions between permanently charges species, or between ion and a permanent dipole There is attraction and repulsion How ionized species interact with water → because water is polar Positive and negative ion will be attracted by water, as water has 2 charged ions: H+ and OCan mix eg salt in water. It can only be mixed, because there is an interaction with water: strong electrostatic interaction between the ions and water molecules who lower the system energy Salt: the ordered crystal lattice /crystal net You put it into water: the water takes all the ions, and pulls everything apart → increases the disorder (entropy= measurement of the disorder), → entropy increases It’s like your room, it always takes energy to organize everything → usually things tend to be higher in Entropy - High entropy in gas, lowest in ice Weak but still important Hydrophic Interactions Refers to the association or folding of non-polar molecules in aqueous solution. This allows: - Protein folding - Protein-protein association - Formation of lipid micelles - Binding of steroid hormones to their receptors - Enzyme substrate → together, repelling water together - Cannot interact with water, cannot dissolve in water Between non-polar molecules that try to avoid contact with water Not a question of the attraction between non-polar molecules, but of the repulsion to water. They’re together because they HATE water - Amphipathic lipid molecules: a molecule with both hydrophilic (water loving) and hydrophobic (water hating) group, such as a lipid molecule - Water around it is super ordered, entropy decreases → thermodynamically unfavorable, therefore hydrophobic solutes have low solubility Non-polar tails of amphipathic molecules join and aggregate so that fewer water molecules are ordered → released water molecules are more random and the entropy (unorderness) increases Phospholipids in water, are organized because they need to repel water together → will form micelles or membranes (nonpolar tails organized inside, while the polar heads are exposed, making energetically favorable H bonds) → only the hydrophilic portion of the molecule is in contact with water, hydrophobic tails are isolated. Makes energetically favorable H-bonds and entropy increases. - - - Hydrophobic effect favors ligand bindings (binding sites in enzymes and receptors) → can bind hydrophobic substrates and steroid hormones Many drugs designed to take advantage of this effect Only biomolecules able to react wit solvents are soluble An OH means that at least that part can interact with water Biomolecules are only soluble if they can interact with the solvent → they need to interact, to eg dissolve Van der Waals interactions - - Based on 2 concepts: o Attractive force: London dispersion (depends on polarizability) o Repulsive forec: Steric Repulsion (depends on atom size) Interactions between molecules but they can be non-polar it’s a simultaneous attraction between one and the other Point at which repulsion is stronger than attraction: minimum enerfy distance or Van der Waals contact distance - Weakest one, easily broken and reversible Universal: between any two atoms that are close together → can be attracted Atoms are constantly moving, at one precise moment, we can find a dipolar moment - o That’s why its so weak. Such a short moment Macromolecules: eg DNA, lots of atoms very close together (nitrogenous bases, etc) → can stabilize Can find in protein structure, enzyme and substrate, etc Osmosis - - Movement of water through a semi-permeable membrane Understand 3 words: o isotonic: equilibrium, no net water movement o Hypotonic: less concentration inside → water goes inside, cell expands o Hypertonic: more concentration outside → goes out, cell shrinks water will move in or out to equalize osmolarity, equation: Π = 𝑖𝑐𝑅𝑇 Ionization of water: weak acids and bases Water is weakly ionized, it can dissociate/ separated into protons and electrons - Equilibrium constant defines the ratio between all species in the equilibrium: Keq= (c)(D)/(A)(B) o if high value of equilibrium constant, high concentration of c and D → so the direction will go to A and B o If low level of Keq: a and b have a higher concentration than c and d pH pH measures the proton concentration of a solution and is based on a logarithmic scale. Pure water: 55.5M → small number, very little dissociated - Formula is 𝐾𝑒𝑞 = [𝐻 + ][𝑂𝐻 − ] [𝐻2𝑂] = 1.8 ∗ 10−16 . We can calculate the ionic product of water: →concentration of Protons x concentration of hydroxide (OH) - In pure water If concentration of protons and concentration of OH are the same → super, duper small If I take this result and do it with negative log→ we get the pH → in water: 7. Neutral because when concentration of protons is the exact same as the concentration of OH. Why is below 7, acidic? We have more protons than OH. Higher concentration of protons → lower pH (acidic) Lower conc. Of protons → higher pH (basic) Why is the pH so important to us? - pH is super important for enzymes and their activity. o Eg. pepsin: around 2 → in stomach, super acidic ▪ will work worse the more basic the pH gets, maybe denatured Acids and Bases - Strong acids and bases are completely ionized in water or fully dissociate. Weak acids and bases are in equilibrium with their conjugate pair. Buffer system: where pH is very stable → 7.3 or something Equilibrium (dissociation) constant: the tendency of a proton donor (acid) to LOSE its proton so: when the Acidic constant is high: pKa= -log ka Strong weak acid: low pka = high ka (high dissociation) → good acid Weak weak acid: high pka = low ka (low dissociation) → bad acid / can’t give many protons - Acid: o under 7 pH o Proton donor o High concentration of protons Can be in the same sentence with different meanings Strong (100% dissociated) weak acid (not all dissociated – part of acid on both sides) - Base o over 7 pH o proton acceptor o low concentration of protons Buffer Systems: - require conjugate acid-base pair TO RESIST CHANGE IN PH buffering capacity lost when pH differs from pKa by more than 1 pH unit if too much of the either strong acid or strong base is added (and the weak one cannot equal it out) there will be extreme changes in pH when pH=pKa, → 50:50 mixture of acid and anion forms of the compound → buffering capacity of acid/anion system peak Titration curves: show conversion of a weak acid to its conjugate base Source: wikibooks Henderson-Hasselbalch equation: allows us to calculate pKa given the pH and molar ratio of acid to base calculate pH given the pKa and molar ration of acid to base and calculate the molar ration given the pKa and pH. [𝐴− ] 𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔 [𝐻𝐴] Biological buffer systems maintain pH in a cell to ensure optimal pH for enzyme-catalysed reactions solubility of polar molecules depends of H-bonds (of acids and bases) and equilibrium between CO2 gas and dissolved HCO3- depends on pH. - Buffer systems in vivo: based on phosphate concentration in millimolar range, bicarbonate in blood plasma and histidine being the efficient buffer at neutral pH.