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University of Toronto Scarborough
Biological Sciences
Shelley A.Brunt

lec02 specific heat 1. heat capacity and vaporization of water a. relatively large amount of heat is needed to raise the temperature of water i. specific heat is the amount of heat needed to raise the temperature of 1 gram of the substance by 1 C b. each water molecule participates in multiple hydrogen bonds that must be broken to increase the kinetic energy of water i. kinetic energy is the energy it possesses due to its motion 1. defined as the work needed to accelerate a body of a given mass from rest to its stated velocity c. biologically relevant: i. multicellular organisms are composed of significant amounts of water ii. resulting in minimization of temperature fluctuations within cells 1. critical since temperature changes alter biochemical reactions iii. amount of heat needed to convert water from a liquid to gas is large iv. evaporation of water absorbs a large amount of heat 1. therefore perspiration is an effective mechanism for regulating body temperature water as a solvent (duplicate) 1. both ionic and polar substances dissolve in water a. they are hydrophilic 2. ions held together by electrostatic forces are weakened by water a. water weakens the interactions between the cations and anions (dissolves the crystal) b. ion electrolytes are soluble until the solution is saturated 3. hydroxyl, keto, carboxyl, and ammonium ion groups confer water solubility via their polar groups a. forms hydrogen bonds with water water as a solvent 1. both ionic and polar substances dissolve in water a. they are hydrophilic i. ions are held together by electrostatic forces 1. water weakens these interactions between cations and anions a. the crystal salt dissolves 2. electrolytes a. two types i. cations ii. anions b. ions i. when dissolved in water, they are surrounded by a solvation sphere of water 1. ions interact with water until saturating at which point crystals saturate out of solution c. polar groups often confer water solubility via hydrogen bonds d. the number of polar groups affects solubility i. the greater the number the more soluble the molecule in water 1. the solubilities of alcohols in water decrease as the non-polar chain increases e. glucose i. five hydroxyl groups and a ring oxygen can form hydrogen bonds with water 1. very soluble 2. attachment of carbohydrates can increase solubility of otherwise poorly soluble molecules such as nitrogenous bases or lipids f. nonpolar substances and hydrocarbons have low solubility in water i. water excludes nonpolar substances forcing them to interact with each other ii. nonpolar molecules are classified as hydrophobic iii. hydrophobic effect is critical in 1. protein folding 2. assembly of biological membrane iv. molecules that have both hydrophilic and hydrophobic regions are called surfactants 1. e.g. detergents a. these molecules are called amphipathic i. greater than 12 carbon hydrophobic chain ii. e.g. 1. soaps: alkali metal salts such as sodium palmitate cellular concentration and molecular crowding 1. diffusion a. only water in cytoplasm i. no contact ii. random pathing towards destination b. crowded cytoplasm (molecular crowding) i. 10x slower pathing towards destination due to factors 1. viscosity 2. transient interaction to charged molecules 3. collisions sodium dodecyl sulfate 2. detergent which has a hydrophobic chain of 12 hydrocarbons and a polar sulfate group 3. micelles a. form when high concentration is dispersed into the water rather than on the surface b. it is an aggregate of surfactant molecules dispersed in a liquid colloid c. trap water insoluble grease and oils within the hydrophobic interiors of micelles, releasing them from greasy surfaces d. in aqueous solution, amphipathic molecules may form i. monolayers on the surface ii. micelles iii. bilayer vesicles noncovalent interactions 1. all are weaker than covalent bonds a. covalent bonds formed by the sharing of electrons between adjacent atoms 2. noncovalent interactions a. hydrogen bonding in water b. hydrophobic interactions 3. weak interactions critical in structure / function of macromolecules such as proteins and nucleic acids a. e.g. double stranded DNA 4. four types a. hydrogen bonding b. hydrophobic interactions c. charge-charge interactions d. van der waals forces 5. variations of electrostatic interactions a. hydrogen b. charge-charge c. van der waals charge-charge interaction 1. interactions between two charged groups 2. strongest non-covalent interaction 3. can allow interactions across a greater distance than other non-covalent interactions a. e.g. NaCl crystals are stabilized by inter-ionic attractions (i.e. charge-charge interactions) 4. strength of charge-charge interactions depends on the solvent a. water greatly weakens the NaCl interaction 5. the stability of biological polymers in an aqueous environment is not greatly dependent on charge-charge interactions a. but electrostatic interactions are critical in molecule recognition i. e.g. reactions of proteins with functional groups b. attractions between opposite charged functional groups on proteins are often called salt bridges or ion pairing 6. charge-charge interactions also responsible for repulsion of similar charged ionic groups hydrogen bonds 1. hydrogen bonds between or within macromolecules compete with water 2. hydrogen bonding between complementary bases a. in order for hydrogen bonding to form between or within biochemical macromolecules the donor and acceptor groups must be shielded from water b. usually buried in the hydrophobic interior of the macromolecule c. e.g. DNA and hydrogen bonding between complementary bases van der waals forces (20-25 minutes late) 1. interactions between permanent dipoles of two uncharged polarized bonds a. or interaction between permanent and transient dipole induced in neighboring molecule 2. weak intermolecular forces between all neutral atoms by transient interactions of atoms that are close together 3. involves both attractions and repulsions 4. weak interactions that cumulatively play an important role in maintaining structure a. e.g. stacking of bases in the DNA double helix 5. concept a. the basis of a van der waals interaction i. distribution of electronic charges around an atom fluctuates with time 6. base stacking interactions a. bases are aligned so that the vertically adjacent base is stacked on top of the previous base b. due to dispersion attraction (van der waals / hydrophobic / electrostatic forces) c. base stacking effects are important in the secondary and tertiary structure of RNA i. provides stability d. in DNA double helix of 3.4 nm corresponds to van der waals contact distance e. base stacking removes non-polar surfaces of bases out of water into contact with each other i. hydrophobic effect 7. electrostatic interaction in DNA a. phosphate i. bears negative charge 1. interact unfavorably with one another over distances ii. when two strands come together, the unfavorable interactions are decreased by the presence of water, Na+ and Mg2+ in solution 1. unfavorable interactions  negative phosphates on nucleotides repelling each other 2. cations (Na+ / Mg2+ in aqueous solution) reduce the repulsion forces inherent in DNA molecules most important noncovalent interactions in biomolecules 1. hydrophobic interactions are mid range in terms of strength a. increased entropy of the surrounding water rather than on direct interaction of nonpolar groups i. important in protein folding 1. causes linear polypeptide to fold into a compact structure due to removal of hydrophobic surface area (which is being packed into core of protein during folding) molecular complementarity 2. binding of proteins via noncovalent interactions a. two proteins are able to bind one another more readily via various noncovalent interactions i. ionic bond ii. hydrogen bond iii. hydrophobic and van der waals interactions review 3. physical properties 4. chemical properties of water are critical since water can react with biological molecules 5. electron rich oxygen is critical since it has two unshared pairs of electrons a. makes it nucleophilic i. it is a weak nucleophile ii. but found in high concentration 1. expect that many macromolecules will be easily degraded by nucleophilic attack by water a. e.g. proteins are hydrolyzed by water to release amino acids 6. important reaction is to hydrolyze proteins a. not in condensation of proteins i. condensation is not thermodynamically favored how do cells prevent the constant degradation by water of macromolecules? 1. if equilibrium is in direction of hydrolysis, how do we make macromolecules? a. the answer is in the nature of the cellular makeup i. the amide bonds of proteins and ester linkages of nucleic acids are relatively stable at the pH and temperature of the cell 1. this reduces their rate of hydrolysis even though hydrolysis is thermodynamically favorable based on the gibbs free energy ii. ATP is used to drive the reaction 1. overcoming the unfavorable thermodynamic barrier important property of water is its tendency to ionize 2. creating charges that will allow other electrostatic interactions 3. pure water consists not only of h2o but of low concentrations of hydronium ions and equal concentrations of hydroxide ions a. hydroxide ions can accept a proton and be converted back into a water molecule i. proton acceptors = bases b. water can function as an acid or base 4. nucleophilic attack of oxygen on one of the protons in adjacent water pH 1. biochemical processes are affected by the concentration of protons 2. the concentration of H+ in cells is small a. but there is a large range of [H+] in aqueous solution 3. use pH to measure concentration of H+ 4. definition of pH and pKA a. pH = log 10/[H+]) = -log 10+] b. pKa = -logKa = log(1/Ka) c. Ka = [H+][A-]/[HA] 5. pKa of an acid is the pH at which it is half dissociated, when [A-] = [HA] a. important because amino acids have different pKa i. by extension, proteins have different pKa
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