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MCDB 310 1st Edition Lecture 2 Outline of Last Lecture I. Review of biological and chemical foundations of biochemistry Outline of Current Lecture I. Water and its importance for lifeII. Non-covalent molecular interactionsa. Hydrogen bondsb. Ionic bondsc. Hydrophobic Interactionsd. Van Der Waals focesIII. Amphipathic CompoundsIV. pH, acids, bases, and buffersCurrent LectureI. Water and its importance for lifea. The human body is 65% water, the earth’s surface is 70% water b. Water’s unique structure makes life possiblei. It is a bent molecule (tetrahedral geometry-bond angles of 104.5 degrees)ii. It is a polar molecule with a partial negative charge on the oxygen and partial positive charges on the hydrogens, creating a dipoleII. 4 types of non-covalent molecular interactionsThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.a. Electrostatic interactions are governed by Coulomb’s Law (determines the force of one molecule on another)i. F=force of one molecule on anotherii. q1 and q2 = two electrical charges (one for each molecule)iii. epsilon 0 = constant of proportionalityiv. epsilon r = dielectric constant of solvent (water=78.5, benzene=4.6)v. r = distance between chargesb. Hydrogen Bonding: and electrostatic interaction caused by partial charges i. Directional: requires 3 atoms to line up linearly (want to keep the partial negative charges as far away from each other as possible)ii. 3 atoms: one electronegative hydrogen bond acceptor (not covalently bonded to the hydrogen), a hydrogen, and an electronegative hydrogen bond donor (covalently bonded to the hydrogen)iii. Hydrogen bonds are much weaker than covalent bondsiv. Biochemical examples:1. Interaction between a hydroxyl group (alcohol) and water2. Interaction between a ketone and water3. Interactions between peptide groups in polypeptides4. Interactions between complimentary bases in DNAv. Hydrogen bonds are essential for:1. aqueous acid/base interactions2. the structure and function of polypeptides, DNA, mRNA/tRNA3. Interactions of water with itselfvi. Crystalline structure of solid water (ice) is due to hydrogen bonds1. Each water molecule hydrogen bonds with 4 surrounding water molecules2. “perfect” crystal structure of ice is at the expense of lower packingdensity (this makes ice less dense than liquid water)3. only 15% of hydrogen bonds are broken when ice melts (remaininghydrogen bonds in liquid water cause high boiling point)vii. Solubility is a solute’s ability to interact more strongly with water than with other solute molecules1. Hydrogen bonds cause polar, uncharged compounds to dissolve readily in water (hydrophilic)2. Solute/solute hydrogen bonds are replaced with solute/water hydrogen bonds3. Dissolving is an entropy driven process because increasing randomness drives dissolutionc. Ionic Bonding: electrostatic interaction caused by full charges (transfer of electrons)i. Again, this electrostatic interaction is governed by Coulomb’s Law (if the epsilon R is high, like in water, the electrostatic force will be low)ii. Water therefore shields electrostatic interactions (reduces the attractive force between opposite charges)1. Therefore, water dissolves salts very well because its partial charges interact with the full charges on the salt2. Solubility of salts is entropy driven (again, increasing randomness increases dissolution)3. Ionic salts are hydrophiliciii. Ionic interactions are much stronger than hydrogen bondsd. The Hydrophobic Interactioni. Non-polar molecules exhibit this kind of interaction with other non-polar molecules1. Therefore non-polar molecules are insoluble in water (incapable ofhydrogen bonding with water)ii. Examples of hydrophobic molecules: 1. non-polar gases (Carbon dioxide, oxygen gas)2. Organic molecules with long, Aliphatic chains (fatty acids, phenyl groups, oils and other lipids)iii. What happens when you put a hydrophobic molecule in water?1. On its own, water will constantly make and break hydrogen bonds (increasing entropy)2. Immediately surrounding a hydrophobic molecule, water molecules become very ordered (decreased entropy —> therefore,this is very unfavorable)3. For this reason, hydrophobic molecules tend to cluster when in water because it reduces the amount of water molecules that must be highly ordered directly surrounding the hydrophobic molecules (increases entropy)a. This is still not favorable, but it is less unfavorable than individual hydrophobic molecules surrounded by their ownhighly ordered “water barrier”b. It also reduces the size of the hydrophobic region that is exposed to waterc. This tendency to cluster is very important in the body (ie-hydrophobic core in proteins, membranes)e. Van Der Waals Forces: interaction between very small electric dipoles induced on uncharged atomsi. Typically occurs between non-polar moleculesii. These interactions are very weak, however at an optimized distance (twice the Van Der Waals radius) the interactions can become significant (especially when the two molecules are very large)1. Optimal distance is neither too close (would cause steric hindrance) nor too far (not enough attractive force)III. The summation of all 4 types of interactions are crucial for the structure of macromolecules and enzyme/substrate recognitionIV. Amphipathic Compounds: compounds that contain both polar (hydrophilic) and non-polar (hydrophobic) regionsa. Examples: Lipids and amino acids (see figure below)b. Amphipathic compounds will form Micelles (3D clusters with a hydrophobic outerlayer and a hydrophilic interior) because it further increases entropy when they are exposed to wateri. This is due to the fact that no hydrophobic regions are exposed to the water and the hydrophilic regions will interact favorably with the waterc. Amphipathic compounds can also form bilayersi. Again, this is favorable because it increases entropy (no hydrophobic regions are exposed to water)V. pH, Acids, Bases, and Buffersa. Pure water is slightly ionizedi. While it should dissociate into hydrogen and hydroxide ions in theory, the reality is it dissociates into the hydronium (H30+) cation and the hydroxide (OH-) anionii. Pure water is in equilibrium with these two ionsb. The position of equilibrium (whether it is balanced between products and reactants or shifted toward one side or another) is described by an Equilibrium Constant (Keq)i. The


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