BCHM Exam I The lower limit for a cell s dimensions is the minimum number of biomolecules necessary for survival in aqueous solutions The upper limit for a cells dimensions is set by the rate of diffusion of solute molecules o The rate of diffusion would limit how far away from the surface a reaction that requires oxygen can occur and would define the maximum size Phototrophs gain energy from sunlight o Autotrophs use carbon from carbon dioxide o Heterotrophs use carbon from inorganic compounds Chemotrophs gain energy from oxidation of chemical fuels o Organotrophs use organic fuels o Lithotrophs use inorganic fuels The bond angle between carbon and 4 other atoms is 109 5 degrees o The lightest atoms form the strongest bonds Living organisms live in a dynamic steady state System anything within a defined region of space o Universe system surroundings o Isolated system does not exchange matter or energy with its surroundings o Closed system only exchanges energy with its surroundings o Open system exchanges energy and matter with its surroundings Ex is living organisms 1st Law of Thermodynamics states that for every physical chemical reaction the total amount of energy in the universe remains constant 2nd Law of Thermodynamics states that the total entropy of the universe is always increasing Entropy S randomness or disorder in a chemical system Enthalpy H reflects the number and kinds of bonds being broken and formed in a chemical system o Making bonds Delta H 0 o Breaking bonds Delta H 0 Free energy is the amount of energy available to do work Delta G 0 reaction is spontaneous and releases energy Delta G 0 reaction is non spontaneous and requires the input of energy o A non spontaneous reaction will proceed in the reverse direction spontaneously Endergonic requires energy to be carried out Exergonic reaction releases free energy o exergonic refers to negative free energy change while exothermic refers to a release of heat Chemical reactions proceed spontaneously until equilibrium is reached Exergonic reactions drive Endergonic reactions when coupled together Hydrogen Bonds are electronegative interactions between hydrogen and an atom of a much higher electronegativity o 10 covalent overlapping 90 electrostatic o Lifetime of hydrogen bond is 1 20 picoseconds o A single water molecule can form up to 4 hydrogen bonds due to its near tetrahedral shape 104 5 bond angle o Hydrogen bonds are strongest when atoms are in a straight line Hydrogen bonds between water molecules make water liquid at room temperature they give water great internal cohesion Polar molecules dissolve in water because they replace the water water bonds with more favorable water solute bonds Non polar molecules interfere with water water bonds o In aqueous solutions non polar molecules cluster together and form micelles o the ordering of water molecules around the hydrophobic portions of amphipathic molecules result in a driving force called the hydrophobic effect that causes the clustering of these groups together resulting in structures such as micelles Water dissolves salts and charged molecules by weakening their electrostatic interactions thus counteracting their tendency to form together Non polar gases are poorly soluble in water they create a decrease in total entropy o All molecules in solution interfere with hydrogen bonding but polar charged molecules compensate by forming new water solute bonds Van der Waals Interactions occur when 2 uncharged atoms are brought together because their 2 dipoles are weakly attracted to one another o As their 2 nuclei draw closer the electron clouds repel each other Hydrogen bonds ionic bonds and hydrophobic interactions are much weaker than covalent bonds because they are constantly breaking and re forming this contributes to a net decrease in entropy o For macromolecules most stable structure is that in which weak interactions are o Hydrophobic interactions between non polar amino acids stabilize 3 D protein maximized structure o Hydrophobic interactions energetically contribute to Bind hormones to receptor proteins Enzyme substrate interactions Membrane structure 3D folding of proteins Colligative Properties are properties of solutions that depend on the number of molecules in a given volume of solvent and not on the properties identity of the given molecules o dissolved solutes alter the properties of the solvent by changing the concentration of water o Vapor pressure o Boiling melting point o Osmotic pressure Osmosis water movement across a semi permeable membrane o Isotonic solution osmolarity of solution is equal to osmolarity of cell s cytosol Cell neither gains nor loses water o Hypertonic solution osmolarity of solution is greater than osmolarity of cell s cytosol Cell shrinks as water moves out of cell o Hypotonic solution osmolarity of solution is less than osmolarity of cell s cytosol Cell swells as water enters cell o Storing fuel as polysaccharides rather than monosaccharides avoids an enormous increase in osmotic pressure Proton Hopping the continuous release of a proton and it being picked up by a water molecule to form hydronium Weak acids do not completely ionize in water o Acids are proton donors bases are proton acceptors o The stronger the acid the greater its tendency to release its proton and the lower its pka value ADP P ATP H2O is a condensation reaction ATP ADP P is a hydrolysis reaction catalyzed by hydroxylases o An Exergonic reaction increases entropy by producing 2 molecules from 1 Amino acids are covalently joined through a peptide bond to form a di peptide o Linkage is formed by the removal of elements of water from alpha carboxyl group and alpha amino group o It should be noted that the joining of amino acids to form peptide bonds eliminates the acid and basic character of the molecules The only ionized groups in the finished protein will be the terminal amino and carboxyl groups and also any R groups that happen to contain acidic or basic groups o Di sulfide bonds play a special role in protein structure by forming covalent linkages between polypeptide chains 20 basic amino acids that each have a carboxyl group amino group R group and a hydrogen all bonded to a central alpha carbon o Non polar alanine valine glycine proline methionine leucine isoleucine o Aromatic phenylalanine tyrosine tryptophan o Polar serine threonine cysteine asparagine glutamine o Charged lysine histidine arginine o Negative glutamate and aspartate Iso electric