CELL AND MOLECULAR BIOLOGY
CELL AND MOLECULAR BIOLOGY BIOL 1441
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This 6 page Class Notes was uploaded by Laurine Pollich on Thursday October 29, 2015. The Class Notes belongs to BIOL 1441 at University of Texas at Arlington taught by Lee Frederick in Fall. Since its upload, it has received 32 views. For similar materials see /class/231263/biol-1441-university-of-texas-at-arlington in Biology at University of Texas at Arlington.
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Date Created: 10/29/15
Important Concepts in Biology What is the difference between polar and nonpolar covalent bonds In order to answer this question begin with the basics what is a covalent bond Two atoms in a covalent bond share electrons Remember electrons like to be in pairs Each atom contributes an electron so there are two which both atoms share The electrons will spin around one atom then the other Electrons are always in constant movement meaning they never stop orbiting the atoms The electrons can spin around the atoms two ways 1 spending more time around one atom than the other or 2 spending the same amount of time around each atom Scenario 1 describes a polar covalent bond Scenario 2 describes a nonpolar bond POLAR COVALENT BONDS Polar covalent bonds result from atoms sharing the electrons unegually This depends on each atom s 39 39 value quot39 U 39 39 is a measure ofan atom39s ability to draw its bonding electrons to itself Each atom has a numeric value corresponding to its electronegativity Electronegativiiies of the Elements 4 mm m m rm mm 2 The more electronegative an atom the more it will attract or quotpullquot the electron to itself Meaning the electrons spin around the electronegative atom more than the other atom it is bonded to Think of the electronegative atom like a bully it does not play nice It is an electron hog It does not like to share How do I determine the electronegativities ofthe atoms Good question I do NOT expect you to memorize those values on the chart above save that for chemistry class I m going to make it easy on you amp tell you which ones are the most electronegative The two most electronegative atoms that we deal with in biology are OXYGEN and NITROGEN These guys are the bullies the electron hogs Carbon and hydrogen are often associated with these bullies because C H O amp N are the four most common elements that compose all living matter Carbon and hydrogen have similar electronegativities They are not bullies when bonded together they cannot pull the electron more than other one can Oxygen and nitrogen are both more electronegative than either carbon or hydrogen If you covalently bond a hydrogen atom with an oxygen atom or a hydrogen atom with a nitrogen atom what do you think will happen You guessed it oxygen and nitrogen will hog those electrons from poor little hydrogen Oxygen and nitrogen will also hog those electrons from carbon What is the consequence of one atom being more electronegative than the other in a covalent bond Well consider that the electrons are negatively charged If the electrons are spinning around the more electronegative atom O or N more often compared to the other atom H or C than the electronegative atom gains a partial negative charge and leaves the other atom with a partial positive charge NONPOLAR COVALENT BONDS Nonpolar covalent bonds result from atoms sharing the electrons egually The atoms in this type of covalent bond have the same level of electronegativity Meaning the electrons spin around the both atoms the same amount of time These atoms play nice they share their electrons equally Because the electron is spinning around both atoms equally there are no partial charges associated with either atom even though the electron has a negative charge REMEMBER Carbon and hydrogen have similar electronegativities so when they covalently bond electrons are shared equally and there is no charge nonpolar Examples C C nonpolar OH polar HH nonpolar OC polar OO nonpolar NH polar NN nonpolar NC polar C H nonpolar Don t worry about ON won t ask that technically it is polar How does polarnonpolar relate to hydrophilichydrophobic Hydrophilic means water quotlovingquot and hydrophobic means water quotfearingquot phobia Molecules that have polar covalent bonds have a partial charge associated with them and may be called polar molecules Water is called a polar molecule because the oxygen creates two polar covalent bonds with the hydrogens Molecules that have charges are attracted to each other positive and negative charges attract This includes molecules that have polar covalent bonds partial charges associated with them and ions charged molecules or atoms due to gaining charge or losing charge an electron These charged molecules or ions dissolve in water Like dissolves like In this case charged water dissolves molecules with charges they are alike bc they both have CHARGES We call these charged molecules or ions hydrophilic water loving bc they are attracted to water and interact with it An example would be alcohols which have a hydroxyl group OH The hydroxyl group is a polar covalent bond between oxygen and hydrogen That functional group has a partial charge associated with it and interacts with water Alcohols and other molecules with hydroxyl groups are hydrophilic and readily dissolve in water Molecules with nonpolar bonds have no charge and referred to as nonpolar Because nonpolar molecules have no charge no re ion of or they do not interact with water which is polar and has a charge We therefore consider nonpolar molecules hydrophobic or water quotfearingquot An example would be hydrocarbons hydrogen and carbon play nice and SHARE the electron equally and therefore have no charge associated with them Fats are mostly hydrocarbons fatty acids and tend to repel water like oil floating on top of water What if you put a protein with amino acids that have side groups R groups with polar and nonpolar functional groups into an aqueous solution waterbased The amino acids with polar side groups OH COOH CO NH2 SH all have polar covalent bonds and like to interact with water Amino acids that have a charged R group ion will also interact with water The amino acids with nonpolar side groups CH3 will not want to interact with water The protein will fold accordingly to its amino acids quotpreferencesquot The amino acids with polar side groupsions all charged will be the exterior while the amino acids with nonpolar side groups no charge will fold to the interior Remember like dissolves like So charged solutionsmolecules will mix with other charged molecules and uncharged solutionsmolecules will mix with other uncharged molecules BUT charged and uncharged will not mix with each other How can I tell which amino acid is polarnonpolar or hydrophilicphobic Amino acids are classified only by their side groups R groups Every amino acid has an amino group orange box below an asymmetric carbon except glycine a carboxyl group yellow box a hydrogen and an R group white box The amino acid quotskeletonquot or backbone is the amino group asymmetric carbon carboxyl group and hydrogen because it is the EXACT same for every amino acid The only difference between the amino acids is their Rgroups Generic Structure of every amino acid Amino Acid backbone in purple R group in white 3 0mm 539 H3thcAC HsNtiCC H3NWC7C l 07 l O I H H H If the amino acid R group can form a hydrogen bond or has a charge ion it is POLAR Identi the functional groups that make up the R group Every functional group is polar except the methyl group CH3 If you read above you already know this because remember carbon and hydrogen play nice and share electrons no charge nonpolar If there is a hydroxyl carboxyl carbonyl thiol functional group it is most likely classified as a POLAR amino acid which is hydrophilic If the R group not the backbone has a charge it is POLAR If it has only methyl groups or hydrocarbon chains CH it is nonpolar and therefore hydrophobic What if it has a polar and nonpolar functional group In this case it is still classified as polar because it will be able to form a hydrogen bond with other molecules Examples below observe the functional groups Polarhydrophilic Polar hydrophilic Nonpolar hydrophobic O O C EH CH 2 O CH CH l 1 O 1 0 HNC7C H N CC 3 3 C C 3 H O l 0 H O H pH Problems recall indicates concentration pH is simply the concentration of hydrogen ions in a solution H ie how many H are in that solution A solution at standard conditions will always have a product of H and OH equal to 10 M Recall product means you multiply two numbers 12 is the product of 3 x 4 That means if you count all the H and then you count all the OH and multiply those numbers they will equal 10 M or 000000000000001 mol L We cannot easily work with those numbers so we use the log scale to measure the concentration of hydrogen ions in solution pH does NOT measure the hydroxide ion concentration pH log H We can determine the hydroxide ion concentration if we know they hydrogen ion concentration and vice versa How Their product is always 10 14 M Math when multiplying two numbers with the same base keep the base the same add the exponents 10395 x 10399 103914 10393 x 103911 103914 10396 x 10398 103914 Get it The exponents have to add up to 14 When dividing two numbers with the same base keep the base the same subtract the exponents 10391410395 10399 103914103911 10393 1014 10398 10396 14 5 9 Got it Why didn t you tell me this was so easy Rule Example 32 3 2 5 Two l1ke s1gns become a positive Sign 63 6 3 9 r 72725 Two unhke s1gns become a negatlve Slgn 862 8 2 6 If you need a math refresher on exponents try this site MI I 39 I 39 hlnccnnt rnm 2005Crl html Examples You have a solution with OH 10 M what is the H Look at the exponent 14 4 10 Answer H 10 10 M What is the pH of this solution The pH of the H is simply the exponent associated with the H no negative signs just the number Answer pH 10 Why isn t the answer 4 Because 10 4 M is the concentration of OH not H pH is a measure of the H concentration NOT OH Why isn t the answer 10 Because pH log H so a x 10 10 See the rules above Keep it simple The log of any number with a base of 10 is simply the exponent In this case it will always be a negative exponent and you will always multiply it times another negative sign so it will always be a positive whole number H 10395 M pH 5 H 10397 M pH 7 NOTE This only works with the H not the OH OH 10 10 M pH 4 H 10394 M OH 10393 M pH 11 H 103911 M You have a solution with a pH of8 What is the hydrogen ion concentration Answer H 10 8 M Just make the pH number an exponent and put a negative sign in front of it What is hydroxide ion concentration of this solution Answer OH 10396 M 14 s 6 Is this solution acidic or basic Answer Basic H 000000001 M OH 00000001 M this is the bigger number remember 8 is smaller than 6 There are more hydroxide ions than hydrogen ions in solution therefore it is a basic solution If there are more hydrogen ions in solution than hydroxide ions it is an acidic solution pH 16 is ACIDIC solution more hydrogen ions in solution than hydroxide ions pH 7 is neutral hydrogen ions equal hydroxide ions in solution pH 814 is BASIC solution more hydroxide ions in solution than hydrogen ions Do NOT confuse the functional group hydroxyl OH with the hydroxide ION which is OH The hydroxide ION is a covalently bonded oxygen to a hydrogen with an extra electron it is an ION a charged molecule A hydroxyl group is a functional group with a polar covalent bond between oxygen and hydrogen AND whatever other atom the oxygen is bound to It is NOT an ion It does not have an extra electron It has a partial charge due to the polar covalent bond If you are struggling with the math please go back to elementary school or high school and apologize to your math teacher who you complained to repeatedly llWhy do I have to learn this stuff I m never going to use itquot
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