Week 3 Notes
Week 3 Notes BIOL 101 - 001
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This 14 page Class Notes was uploaded by Caroline Colleran on Sunday September 13, 2015. The Class Notes belongs to BIOL 101 - 001 at University of South Carolina taught by Vicki S Vance (P) in Fall 2015. Since its upload, it has received 42 views. For similar materials see Biological Principles I in Biological Sciences at University of South Carolina.
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Date Created: 09/13/15
BIOLOGY 101 VANCE Introduction CHAPTER 1 Biology study of life Unifying themes in biology help to organize all of the information helps to remember it and to think about it 1 Life is organized on many structural levels a Start at the simplest level increasing complexity b Atoms l molecules l macromolecules l cell structures l cells l tissues l organs l whole organism l populations l communities ecosystem 2 Emergent properties as you move up in complexity new properties emerge 3 Cellular basis of life cell theory 2 parts a All living things are made of cells b All cells come from other cells 4 Heritable information a DNA is the genetic information in cells b The information in DNA ows in 2 ways 1 parent I offspring gt it is DNA that moves from parent to the offspring 2 DNA l RNA l proteins c DNA has the code for how to make proteins It is the proteins that determine what an organism is and what it can do 5 Correlation of structure and functions a What a molecule looks like determines what it can do 6 Unity in diversity 15 million species identi ed estimated 30 million species exist HUGE DIVERSITY a Unity in life yet all living things share certain traits i Ex Genetic code same in all living things ii Glycolysis series of chemical reactions that use food to produce readily useable energy Theory of Evolution greatest unifying theme in biology Explains both diversity and unity in life BIOLOGY 101 VANCE CHAPTER 2 Atoms molecules and chemical bonds Unity because all living things today are connected because they came from a common ancestor in the ancient past Diversity because living things have changed to t a particular environment 825 Matter elements amp compounds anything that takes up space and has mass a Element can t be broken into other substances by ordinary chemical means 92 naturally occurring elements i 25 elements required for life ii 4 elements make up 96 living matter Carbon Oxygen Hydrogen Nitrogen b Compound molecules made up of more than one element in a xed ratio i Ex NaCl sodium chloride Structure amp Behavior of Atoms a Atom smallest possible amount of an element b All atoms of an element are alike c Each element has its own kind of atoms i Ex C and H atoms are different from one another d Atomic Number of protons in an atom e Atomic mass of protons of neutrons how much it weighs f Isotopes atoms of an elements that have different atomic mass but some atomic different number of neutrons i Some are unstable radio isotopes ii Release energy as they break down iii They can be useful Electrons amp Energy Levels a Where electrons are found orbiting nucleus of atom at discrete levels positions called shells b Electrons ll up closest shell rst 2 electrons c Outer shells lled in order next one holds 8 d If atom doesn t have enough electrons to ll all shells only outermost shell is partly empty e Octet Rule all atoms have tendency to ll up the outer shell i Ex Noble elements f Chemical properties of an element depend on of electrons in outermost shell Chemical Bonds attractions that hold atoms together a Molecule 2 or more atoms held together by chemical bonds BIOLOGY 101 VANCE b Valence bonding capacity of an atom of bonds an atom must form to be stable of electrons needed to ll outermost shell STRONG BONDS A Covalent Bonds a chemical bond formed by sharing electrons STRONG BOND a 2 Kinds nonpoar covalent bonds amp polar covalent bonds b Nonpolar Covalent Bonds bond formed when two atoms with similar or identical electronegativity share a pair of electrons c Electronegativity ability to attract electrons i NaltHltCltNCltO ii Low ability to attract electrons high ability to attract electrons d Nonpolar Bond 2 atoms share a pair of electrons equally because about the same ability to attract the shared electrons e Polar Covalent Bond share electrons unequally i One atom has greater electronegativity it hogs upquot the electrons and therefore is a little bit negatively charged ii Other atom is cheated out of shared electrons much of the time and therefore is a little bit positively charged iii Usually nd POLAR COVALENT BONDS in molecules involving H with O N Cl iv Ex H20 f Single covalent bonds atoms share 1 pair of electrons g Double covalent bonds atoms share 2 pairs of electrons h Triple covalent bonds atoms share 3 pairs of electrons B Ionic Bonds bond formed by electrostatic attraction between two atoms after a complete transfer of an electron from a donor atom to an acceptor atom STRONG BOND aExNaCl V Chemical Reactions the breaking and forming of chemical bonds described chemical equations that tell what atoms are involved how many which way reaction goes a Most biologically important reactions are reversible and reach an equilibrium WEAK BONDS Some are important for Biology BIOLOGY 101 VANCE A Hydrogen Bond weak charge attraction between a positive H atom of one molecule and a negative atom of another molecule a Ex H20 no electron sharing i No electron transfer ii Weak bond iii 120 strength of covalent bond iv continually breaking and forming B Hydrophobic Bond tendency of nonpolar molecules to avoid H20 a polar substance and thus associate with each other a Ex Important in membrane structure Chapter 3 Water Life began as water all organisms made up mostly of water 34 of Earth is made up of water The abundance and unusual behavior of H20 is the major reason the earth is habitable The unusual behavior is due to hydrogen bonding H20 is a polar molecule due to polar covalent bonds between 0 and H charge on H H charge on O H20 molecules are attracted to one another and to other polar or charged molecules due to charge attraction Unusual properties of H20 are an example of EMERGENT properties due to an increase in level of structural organization caused by H bonding Unusual Properties of Water H20 a High Speci c Heat amount of heat in calories required to increase the temperature of a substance by 1 degree Celsius i With H20 heat goes rst to break Hbonds therefore little change in temperature ii If you take out heat Hydrogen bonds form releases heat little change in temp iii Biological signi cance of high speci c heat 1 Living organisms are made up mostly of H20 and can therefore resist dramatic changes in temperature 2 This tends to stabilize ocean temperatures and protect marine organisms b H 20 expands When it freezes therefore ice oats on liquid water i H20 is one of only a few substances where the solid form is LESS dense than the liquid forms ii Due to Hbonding between H20 molecules BIOLOGY 101 VANCE iii In liquid H20 Hbonds form and break often as the molecules move around iv At 0 degrees Celsius the molecules are no longer moving fast enough to break Hbonds the H20 molecules become locked into a crystal lattice where each H20 is bonded to the maximum of partners held farther apart from each other less dense v Biological signi cance of ice oating oating ice insulates the liquid water below prevents lakes and oceans from freezing solid allows survival of water organisms during winter c Water is the Biological Solvent i Solution liquid which is a homogeneous mix of 2 ore more substances 1 Solute substance that is dissolved 2 Solvent the dissolving agent ii H20 is the solvent in living organisms iii The cell is like a tiny drop of H20 with many molecules solutes dissolved in it iv The characteristic properties of H20 as a solvent are due to Hbonding v H20 is a good solvent for charged or polar substances opposite charges attract vi ex NaCl easily dissolves in H20 the polar H20 molecules pull the 2 ions apart and surround them n E EJ39I Ea ii mi quot r 1 If L r 1 1 39t g at i x ft L l a i I x l u n J Lu ll1 395 M ml 1 Equot L6quot quot39 i i 39t if rial L it vii Nonpolar substances do NOT dissolve in H20 polar and nonpolar substances do not mix like oil and H20 oil is nonpolar and H20 is polar ll Properties of Aqueous Solutions solutions where H20 is the SOLVENT cells are aqueous solutions so it is important to understand the properties of aqueous solutions we will discuss two properties of H20 solutions A Solute Concentration of molecules in a given amount of solution a Moe of grams of a substance equal to its molecular weight BIOLOGY 101 VANCE an B Acids Bases and pH a b c Molecular Weight sum of the atomic masses of each atom in the molecule Molar of moles of a solute in 1 liter of solution The concentration of substances in living cells is usually given in terms of molar1y This is because molarity gives information about the of molecules One mole of ANY substance has the same number of molecules as one mole of any other substance 22 1 23 molecules quotuh i a quotEvil 6 O X 0 quotifquot Ijtrf39li an The H20 molecule can dissociate This happens rarely Though rare it is important because small changes in H and OH can cause dramatic changes in the ability of biological molecules to function ln pure H20 the H OH they are in balance When acids or bases dissolve in water it shifts the balance of H and OH ln pure H20 H OH 10 7 Chapter 4 Carbon and Molecular Diversity Most biologically important molecules are carbonbased Carbon element of life Why Carbon gt gt Small Versatility in bonding can bond to other carbon atoms or to forms strong bonds 4 covalent bonds several other elements gt Good transport form 0 Carbon Dioxide is a gas that easily crosses membranes gt Organic Molecules Organic Chemistry compounds contrast with 5102 sand Carbon can form large complex and diverse molecules molecules that contain carbon branch of chemistry that studies carbon Properties of organic molecules depend on arrangement of carbon atoms in molecules Carbon Skeleton Variations in Carbon Skeleton gt Length how many carbon atoms gt Shape straight chain branched chain ring BIOLOGY 101 VANCE gt Location amp number of double bonds gt What other elements covalently bonded to skeleton lsomers compounds with same molecular formula but different structures 3 Different Structures 1 Structural isomers different in covjalent arrangement of atoms C H H i l l 1 will if H a W H u n 2 Geometric lsomers samelgoyhalent bonds butdifferent spatial arrangement amp ll l r a Ex C202H4 lib in l 9 J U b Will not allow rotatiorkir I39IT l H 3 Optical lsomers 5tereoi50mer5 isomers that are mirror images of each other a Can occur when there are 4 different atoms or groups of atoms bonded to the same carbon atom b A carbon atom with 4 different atoms bonded to it is called an asymmetric carbon c D or L isomers d Examples amino acids and sugars Hydrocarbons molecules containing only C and H gt Major components of fossil fuels gt They are nonpolar and don t dissolve in water gt Nonpolar covalent bonds Functional groups speci c groups of atoms bonded to the carbon skeleton gt Each functional group confers speci c chemical amp physical properties gt Usually involved in chemical reactions 6 Functional Groups know the structural formula for each BIOLOGY 101 VANCE Mama tingquot Er n m 39 quotquot39I i I 39 I I H m out t C39E tigi H Tc39vE mww h quota hr 9w It all 7 n 1 x m ark5 39 n l V 39 EFL in39ql I H h I n v 1 amp1 3 Km 1 G34 L Elmslut 1 l4 l 39 U quot g quot 139li quot 39iquot quot3 LEM lhm39l E 1L4 392 quotf1th EliaF39theIJL i l3quot if Bigfut 39 39 39a quota quotquot a I quot 11 5471 3 uhquot It 39kie f EH F 39 39l mmv a if Stills l h 139 E39 L quot quot LW39 rift if he 3 E If 5 l s 3L l EH ef Tm a l Lear gagleli h a 7 L fl m I a 39H r ill 33 w a u n i a 1 quotr3139Is r u u 3f I A Ell i cnl lii full r quotH r u I r CIR M l t r h im VLW q I I HI r gt H V 4 IVH l TM a El IlbAJI39E ug v 4U H 3 Fr lp r I K h K L Li Pm Ctr a Hf 53quot quot toms NIH1quot a x b warrant gm Eli3 H riiwmmm 545 g full cw39 T 1 I I I l Ir r t7 lquot bre ll l le iwn JFVGTErI L hgiquot51t139lqh a mum u Fitx 9 v 39L J kl a H quotk ell flf39fti r39x LETl 545 Ill I I Emmi 13 I lr it th LU LJ1I39 la 5 Lquotquot39 quotJquot quotquotquot39 r r 39 l f c r H L Lt qu VP a n 3 1 Ir v I 39 39 ejLGth lg mrh t int EULWJ quot J39 LI Flam 31 l39vmiithL Lint 5 w names rot groups structures and how they re attached to the carbon skeleton except for phosphate and characteristics conferred by the group Chapter 5 Macromolecules 4 major types proteins carbohydrates nucleic acids and lipids Know the structure of each be able to recognize them Large organic polymers large molecules made from many identical or similar subunits connected by covalent bonds Subunit monomer building block BIOLOGY 101 VANCE Polymers are formed from monomers by a common chemical process Dehydration Synthesis removal of H20 gt One monomer loses a hydroxyl group OH gt Other monomer loses a hydrogen atom H After dehydration synthesis the 2 monomers are covalently bonded to each other and the H20 molecule is released Requires energy Requires biological catalyst enzymes Polymers are broken down into monomers by the opposite process Hydrolysis The covalent bonds holding monomers together are broken by the addition of an H20 molecule gt One monomer adds a OH group gt Other monomer adds a H group gt The 2 monomers are now separate gt Hydrolysis RELEASES energy Proteins polymers of amino acids connected by peptide bonds KnoW the group name of the monomer and name of the bond for each macromolecue protein amino acid peptide bonds Be able to recognize a molecule of that group Be able to draw a circle around one monomer and an arrow around the bond gt Each protein has a unique 3D shape gt Examples of protein functions 0 Structural support 0 Transport of molecules l ex Hemoglobin major protein in red blood cells l carries 02 and C02 in the blood 0 Movement contractile proteins on muscle cells 0 Biological catalysts enzymes Amino Acids monomers of proteins there are 20 common ones to make up protein gt Exist as optical isomers BIOLOGY 101 VANCE n39 Iquot H i39 i J In I i 391 i I Vquot In 32 15 39H it i is I I l setlick l i was i i quotH 239 I i 139 a a I V II n k quotaquot a r39l 39 39a r J i i L in I hi e 5 mi I I39Il I AIII K V V I A I I I I 39v DEWi1 i in if cum Ellier a r239 quot II39 n q I I L a I ii I I I LEI nI LL 131 ll I 1 39 H l 1 quot u i ii 3 39 H i tquot i quotin 39 3939 J 1L 339 F5 l 55 II quot EH 39 39ii a a j 3912 AEJL JUIquot 39x in H r39h ti i i airi I if x i i i 3955 r IIEi i nx I H I rr in ii I I I A I a I i 1 Hit M iri m rt L 39 i quot339 P 1 quotLI I a i a lur 4 39L i1 Afrtu i a I v a i n i gt n n lagI n i v a r quota c a 391 Mn quoti I iF39I 5 a I 39 113 iii Li 39 539quot firquoter 39 a 11 m IL Whit 5 5 r a I r r i F I i if tutti i iiig39qfi11i ii39i iai iiWH hath L IS l m I I I Evian I Ii I h h 5 i i HIn F1 H mm a I iii quoti it it itquot this kt t ii w E gt All amino acids have an asymmetric carbon 0 That carbon has 4 different groups of atoms bonded to it gt Because of the asymmetric carbon amino acids can exist in 2 different isomeric forms D amp L isomers gt Usually only the L isomer of amino acids are found in proteins gt i H quot v H Hi i l at a i ya i quot l D HEHt cl c Hakimi c 5 a x H E O r g HE 39 CH Glycine Ely Marlins Mia Feline WEI Lamina Lauri H iii 39E39 ti H o Hawaiihug E HEW E E HEN39 IEIi Cf quot cm i it i i 39x m H A El 5 a NON OLRR ng a H E r 39 J n 1 f a c a a t id iL quot Methionine Met Phenylalanine Pine Trypt phan Trp BIOLOGY 101 VANCE gt AH Eifiiitigm aThmi39ii eiTHri rsteinei ysi quotTimimaiwr i Asparagineiimani A idl 4h r quotan m j Basin emquot 1 n been M39Hi NH Firmf on Basic ru I K mi 394 Fillis2 Asmaraaaiaij napje Glutamic acldui lw Lysinei tyei rgi inei rgt gt Polypeptide chains many amino acids joined together by peptide bonds 0 Each peptide bond is formed by dehydration synthesis 0 quotL II T 3 iii r i ii a w t as h isLiji i iii If Skirim 39 ll 392 quot 39 0 When amino acids are connected by peptide bonds a repeating structure is formed itji ijtfii i1i i39ii E m ALmew w w 1i 1 it Vigil5M1 My fitm atom m 1 i H 9i ll Hii f 39 i39 Q i5 1 A F I H H BIOLOGY 101 VANCE o repeating NCCNCCNCCNCC is called the backbone of the protein 0 2 ends of the protein are different Nterminus amp C Terminus Levels of Protein Structure Primary 1 Structure sequence of amino acids Secondary 2 Structure repeating twisting and folding of the peptide backbone due to hydrogen bonding between atoms in the backbone repeated NCC NOT due to interactions between R groups 0 2 major kinds of secondary structure 0 Helix o Bpleated sheet Tertiary 3 Structure describes the 3D structures due to interactions between R groups 0 3D shape is maintained by weak interactions 1 Hydrogen bonds 2 Hydrophobic interactions between nonpolar R groups found in interior of protein whereas polar R groups are on the surface of protein interacting with H20 0 However some proteins have covalent links that hold the 3D shape of the proteinwtogether if ll 1 I g i p I I quotI 39739 r 76 quotquot n 39quot 39 39quot LIL f i m 39 TI m x r rui39l39n i l39 i it 4 r 39I r laquot 39 V 139 H H L 1 I 5quot Wf39f i 1 3339 1 zquot 33 If E i 3 I t l39 I39 392 I L ELLEquotfl 1 quot Etc i 5 LA l i1 It r39quot quot iji H L Wquot L In x i l l 39a c5 r LL J l fir tii wt1i n I I 7 H E Ila ll rquot l I 0 Iquot39l 2 Quarternary 4 Structure association of more than one polypeptide chain 0 NOT all proteins have 4 structure some are simply a single peptide chain 0 Example of protein with 4 structure is collagen o 3 helical polypeptide chains intertwined into a triple helix 0 This structure is held together by the same kind of forces as 3D shape mostly weak forces BIOLOGY 101 VANCE Protein function depends on 3D shape of the molecule also called Conformation The shape of the protein allows it to recognize and bind to speci c molecules 0 Loss of 3D shape loss of function 0 Loss of 3D shape is called Denaturation The denatured protein still has its primary structure but it is no longer folded up properly into the 3D shape Chapter 5 Carbohydrates Sugars or polymers of sugars Monosaccharides simplest monomer Disaccharides double sugar 2 monomers joined by dehydration synthesis Polysaccharides storage starch glycogen structural cellulose Functions Energy source Energy storage Structural molecules Source of carbon to make other organic molecules A Monosaccharides single sugar a Sugars contain C H O in xed ratio CHZO b 37 carbonssugar molecule common ones triose 3C pentose 5C amp hexose 6C c Each carbon in sugar has a hydroxyl OH group attached to it except one which is the carboxyl carbon C 0 d In H20 these monosaccharides tend to form ring structures ring is favored i Ex Glucose a speci c hexose B Disaccharides 2 monosaccharides joined by a glycosidic bond a Ex Maltose gt 2 glucoses joined by dehydration synthesis i Important disaccharide used in brewing beer b In maltose the glycosidic bond joins Carbon 1 ofgucose to Carbon 4 of another glucose C1C4 c Other disaccharides examples i Glucose 6C Galactose gt Lactose milk sugar ii Glucose 6C Fructose gt Sucrose table sugar C Polysaccharides macromolecules formed by linking 100 s to 1000 s of monosaccharides by glycosidic bonds a Ex Starch major storage polysaccharide in plants a polymer of glucose connected by 2 14 glycosidic bonds BIOLOGY 101 VANCE
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