BSC-114 Chapter 2 Notes
BSC-114 Chapter 2 Notes BSC 114
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This 40 page Class Notes was uploaded by Victoria Lewis on Wednesday February 24, 2016. The Class Notes belongs to BSC 114 at University of Alabama - Tuscaloosa taught by Edwin Stephenson in Winter 2016. Since its upload, it has received 61 views. For similar materials see Principles Of Biology I in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 02/24/16
EXAM 1 NOTES Wednesday, February 24, 201611:07 PM Chapter 2: Atoms,Bonds,and Molecules ○ a ATOM is a fundamental unit of matter,everyatomcontains a nucleus and electrons § Atomic Nucleus contains 2particles: □ Protons □ Neutrons § Electrons orbitthe nucleus Atomic Structure § Protons: Charge of +1 □ # protons determines chemical identity □ Carbonalways has 6 protons,NO OTHERatom has 6 protons □ # of protons=atomic number □ Belong in atomic Nucleus § Neutrons: NO CHARGE □ No role in determiningchemical properties □ # protons+#neutrons= ATOMICMASS □ Belong in atomic nucleus □ Neutrons canvaryin number w/o affecting chemical properties.Atoms withdifferent#s of protons =ISOTOPES ® The same elementcanhave different#s of neutrons □ Belong in atomic nucleus □ Neutrons canvaryin number w/o affecting chemical properties.Atoms withdifferent#s of protons =ISOTOPES ® The same elementcanhave different#s of neutrons ® Isotopes are variants of elements withdifferent numbers of neutrons ® Have same chemical properties ® Some stable ® Unstable isotopes spontaneouslybreakdown into other atoms (carbon14) (Nuclear process) □ Hydrogen 1 doesn’t have neutrons § The number of protons determineschemical identityand properties § Processesthatchange the nucleus are nuclear processes § Electrons: Chargeof-1 □ In an unchargedatom(# of electrons=# of protons) □ Atoms may gainor lose electrons,turningitinto an ion □ Electrons occupyenergylevels "shells" ® Firstshell=2 electrons ® Secondshell=8 electrons ® Third shell = 18 □ Electronshells representenergylevels ® Lowestenergy:shell closestto the nucleus ® Electrons canabsorbenergy,pushing electrons into ahigher shell.Electros give up energy byfallingto its original shell/level (photosynthesis) ® Atoms tendto fill their outer shells with electrons ® Filling outer shells happens in2 ways: 1) FormingCovalentBonds } In a covalentbond atoms share electrons;eachsharedelectron counts towardfilling its outer shells. } Oxygen:8 electrons – 2 electrons in1stshell – 6 electrons in2ndshell (can hold 8) } Oxygen:8 electrons – 2 electrons in1stshell – 6 electrons in2ndshell (can hold 8) } Hydrogen:1 electron – 1 electronin1stshell } Eachhydrogenshares apair of electrons withanoxygensatisfying its 1stshell requirement – H2O } CovalentBond=Strong } Molecules are depictedinavarious ways. – In the most common shorthand, a solidline indicatedcovalent bond } Eachatom makes acharacteristic # of covalentbonds,based onfilling its outer shell } BondingCapacity(valence-number of hydrogen atomsitcan contain) – Carbon: 4 – Nitrogen:3 – Oxygen:2 – Sulfur:2 – Hydrogen: 1 1) Ionization:atomaccepts or loses electrons } Chlorine accepts 1electron (has 7 wants 8) to fill its outers shell---> Cl- } Mgloses 2 electrons (has two wants zero)----> Mg+2or Mg++ } For any givenatom, protonnumber is fixed } Ion= chargedatom (# of protons doesn’tequal electrons) – Positivelychargedion=cation. Negativelychargedion=anion Elements,Compounds,and Molecules □ Element: substance that consists of only one type of atom. ® Calcium,hydrogen – Positivelychargedion=cation. Negativelychargedion=anion Elements,Compounds,and Molecules □ Element:substance thatconsists of onlyone type of atom. ® Calcium,hydrogen □ Compound:substances with2 or more atoms in fixedratio ® Table Salt=NaCl ® CarbonDioxide=CO2 □ Molecule:two or more atoms heldtogether by covalentbonds □ CovalentBond:atoms share one of more electrons CovalentBonds:Polarand nonpolar covalentbonds □ Covalentbond= sharedelectrons."cloud" of electrons orbitbothatoms. ® Electrons maybe sharedequallybtw 2 atoms. ® In other cases electronsharingis notequal. □ Electronegativity:affinityfor electrons,aninherent property of each type of atom. ® A measure of the tendency `of an atom to attracta bondingpair of electrons □ If atoms in a bond have differentelectronegativity, electrons are sharedunequally ® Water □ Polar Covalentbond:unequal sharingof electrons causes bondto have positive and negative poles ® O-H bondin water ® Polar Bonds: O-H,N-H,O-C,etc ® High electronegativityatoms:O,N ® Low electronegativityatoms:C,H ® Make polar bonds whenwe mix these too,a high and a low □ Non-polar bonds:atoms have similar electronegativity, so share electrons equally, so no ® High electronegativityatoms:O,N ® Low electronegativityatoms:C,H ® Make polar bonds whenwe mix these too,a high and a low □ Non-polar bonds:atoms have similar electronegativity,so share electrons equally,so no positive and negative charges ® C-H ® Have the same electronegativity Non-CovalentBonds □ Non-Covalentbonds:much much weaker than covalentbonds,but importantin biology.Types: 1) Hydrogen Bonds:two polar molecules are attractedbyopposite charges,causedby polar covalentbonds ◊ Example:Water-Ammonia ◊ Opposite charges attract:positive is stronguptowardshydrogen ◊ 2) Ionic bond: bond basedon charge attractions,NaCl.Ionic Compounds=salts ◊ Positive and negative charges attract(Na is positive and Cl is negative) 3) Vander Waals attractions:weak attraction when atoms are so close thatouter electrons shells barelytouch ◊ Very weak, only significant when you get many of them ◊ Repeal if theygetto close together ◊ Importantin "lock andkey" types of molecular interactionex:bindingof hormone to receptor ◊ Only significantwhenyouhave a whole bunch together Chemistry vs.Biochemistry-Preview □ Chemistry=breakingandreformingbonds ® Iron+ oxygen= ironoxide (rust) □ Biochemistry=breakingandreformingbondingin Chemistry vs.Biochemistry-Preview □ Chemistry=breakingandreformingbonds ® Iron+ oxygen= ironoxide (rust) □ Biochemistry=breakingandreformingbondingin living systems ® 6 CO2+ 6 H20---> C6H12O6 + 6 O2 (carbon dioxide + water ---> sugar + oxygen) (photosynthesis) ® RNA with 100 nucleotides +nucleoside triphosphate --->RNAwith 101 nucleotides + diphosphate ( transcription) Chapter 3: Water CovalentBonds ○ Electrondistributionfor various charges § Non-polar covalentbond: the two atoms are similar/same inelectronegativity □ C-C □ C-H § Polar Covalentbond:the two atoms are verydifferentin electronegativity □ O-H ○ Solid Line Hydrogen Bonds ○ In a polar covalentbond, eachatomhas a partial charge due to unequal sharingof electronpair. § O-H bondin water ○ Opposite partial charges attract. § Result:water molecules are boundina hydrogenbond lattice ○ DashedLines Properties of Water 1. CohesionandAdhesion § H-Bonds cause water molecules to cohereto each other,stick together andadhere to other polar molecules. □ Cohesion:attractionof the sametype of molecule 1. CohesionandAdhesion § H-Bonds cause water molecules to cohereto each other,stick together andadhere to other polar molecules. □ Cohesion:attractionof the sametype of molecule (watertowater) □ Adhesion:attractionof two differentmolecules (water to another polar molecule) § Relevance to livingorganisms:cohesionaccounts for water transportinplants (acolumnof water is "pulled" throughvascular tissue) surfacetension,etc. 2. Specific heatand heatof vaporization § Water has a high specific heat(amountofenergy absorbedper rise intemperature).Heat=molecule movement.Because water molecules are bound together,large amounts of energyrequire to disrupt lattice. □ 1 Calorie=energyrequiredto raise 1gramof water 1 degree C. □ Relevance to livingorganisms:bufferingfrom temperature fluctuation. § High heatof vaporization(amountofenergytogofrom liquid to gas phase) Water has high heat of vaporization because lattice of boundmolecules inliquidwater resists "escape" into gas phase. □ Relevance:evaporative cooling.Large amounts of heatremovedbyevaporation 3. Ice § Solid H-bondlattice is fixedwith definedcrystalline structure § Consequence: Ice is less dense than water, so ice floats and insulates bodies of water. 4. Solubility § Polar and chargedcompounds dissolve inwater (hydrophilic) □ Surroundedbya shell of water molecules,the hydrationshell □ Hydrationshell helps formthe hydrogenbondof water § Non-polar molecules (no hydrogenbonds) are insoluble in water (hydrophobic) □ Excludedfromhydrogenbondlattice (oils) □ Doesn’t have the hydrogen bond formats to form with water water § Non-polar molecules (no hydrogenbonds) are insoluble in water (hydrophobic) □ Excludedfromhydrogenbondlattice (oils) □ Doesn’t have the hydrogen bond formats to form with water □ Relevance:membranes Chemistry Digression ○ Mostchemical reactionshave anequilibrium,indicatedby double arrows:A+ B C § Compounds A and B to make C, and C breaks down to make A and B § At equilibriumyoufinda fixedratio of (Aand B):C ○ When emphasizingaparticular reactionsometimes asingle arrowis used, usuallywhen a reactionis essentiallycomplete at equilibrium § E + F ----> G ○ Brackets indicate concentrationof the substance enclosed Water ionization ○ Ionization=gainor loss of electrons (NaandCl) ○ Ionization canalso happen when molecules release H+ ○ Water ionization: § H20 H+ + OH - § (arare event:the concentrationof H+andOH- ions are 10^-7 Moles each=about 1 ionized molecule vs.500 billionunionizedwater molecules) § H+ = hydrogenion,or a proton.Mayjoin a water molecule to formahydroniumion(H20+ H+ ----> H20+) § OH- = hydroxide ion ○ In pure water [H+] = [OH-] ○ In solutions the concentrationof H+andOH- can differ: § If [H+] = [OH-], solutionis NEUTRAL § If [H+] > [OH-], solutionis ACIDIC § If [H+] < [OH-], solutionis alkaline,basic 1. Acids and Bases § Measure of acidity/alkalinity § pH= -(log[Hydrogenion]) □ pH of pure water = 7 ® Hydrogenion= 10^7 Mole § An acidis compoundthationnizes to release H+and increases [H+](pH<7) § pH= -(log[Hydrogenion]) □ pH of pure water = 7 ® Hydrogenion= 10^7 Mole § An acidis compoundthationnizes to release H+and increases [H+](pH<7) □ EX: § A baseis a compoundthationizes to release OH-, or directlycombines withH+;both decrease [H+](pH>7) □ EX: □ Ex: § Buffers:chemicals thatresistchanges inpH.A buffer absorbs excess H+when[H+] is high, and donates H+ when [H+] is low □ Ex: § Relevance:pHwithin cells stays within a narrowrange (slightlybasic) Chapter 4: Carbon Carbon Chemistry 1. Organic Chemistry ○ C has a valence of 4. Makes 4covalentbonds.Does not ionize. ○ Organic Chemistry=chemistryof C- containingcompounds Carbon Containing Molecules 1. Models ○ C-containingmolecules are oftenthree-dimensional although drawn as two-dimensional ○ ○ Organic Chemistryshorthand: carbonsandhydrogen often ○ ○ Organic Chemistryshorthand: carbonsandhydrogen often not shown § Assume Cat junctionof two bonds § Assume number of hydrogens to complete 4bonds. ○ This figure shows the same molecules usingthe shorthand § ○ In this figure the circledjunctionis actually: § 2. Examples ○ C makes single,double or triple bonds. ○ Hydrocarbons:consistof carbonandhydrogenonly. ○ Compounds canbe linear,branched,or ringmolecules Functional Groups ○ Reactivityof organic molecules is determinedbyfunctional groups=small molecules attachedto C ○ 6 groups:hydroxyl,carbonyl,carboxyl,amino,sulfhydryl, phosphate ○ 1 more:methyl (nota functional group,butimportantin biology) 1. Hydroxyl ○ Polar,forms hydrogenbonds ○ Characteristicsof alcohols 2. Carbonyl ○ Electronegativityof C<O, so C=O bonds are polar (forms hydrogen bonds) 1. Hydroxyl ○ Polar,forms hydrogenbonds ○ Characteristicsof alcohols 2. Carbonyl ○ Electronegativityof C<O, so C=O bonds are polar (forms hydrogen bonds) 3. Carboxyl ○ (ahydroxyl plus a carbonyl) Hydroxyl ionizes to -O-, releasingH+ ○ ○ Because itincreases the concentrationof H+.It is an acid (acetic acid) 4. Amino ○ -NH2 ○ Ionizes:accepts a free H+to become NH3+.Decreases H+ concentration,so itis a base(decreases hydrogenions) ○ Amino acids 5. Sulfhydryl ○ S-H ○ Importantin proteinstructure:two sulfhydryl groups makea covalentbondto crosslink proteins. ○ Sulfhydryl undergo achemical reactionwhentwo combine 6. Phosphate ○ -PO4 ○ Valence of phosphorus=5 ○ Non- ionized structure: ○ An acid:-OH ionizes to -O § -PO4is the acidin deoxyribonucleic acid(DNA) 1. Methyl (HONORARY) ○ CH3 ○ Notrelative,so not reallya functional group ○ Oftenadded to biological molecules to modify structure/function Depictionof organicmolecules • Shorthanddepictions oftenassume thatthe reader will apply knowledge of organic chemistryto infer the structure structure/function Depictionoforganicmolecules • Shorthanddepictions oftenassume thatthe reader will apply knowledge of organic chemistryto infer the structure Isomers • Isomer:compoundwiththe same chemical formula,butdifferent structures • 3 types: 1. Structural Isomer § Differentinarrangementof covalentbonds,have the same formulabuthave differentstructures § Pentane and 2-methyl butane both have formulaC5H12 but differentstructures 2. Cis-trans Isomer: § Differentatomarrangements aroundadouble bond. Inflexibilityof the double bondmakes these different § Cis: onthe same side.Trans:on opposite sides. § Cis-trans isomer is also knownas geometric isomer 3. Enantiomers § Different arrangement of atoms of groups attached to an asymmetric carbon § Asymmetric carbon has 4 different functional groups attached. § Chemical mirror images= identical chemical properties § Biological relevance: usually only one enantiomer is found in biological molecules (all amino acids in proteins are L amino acids) § 2 properties: 1. carbon that is making bonds to 4 things 2. making bonds to 4 DIFFERENTthings § Biological relevance: usually only one enantiomer is found in biological molecules (all amino acids in proteins are L amino acids) § 2 properties: 1. carbon that is making bonds to 4 things 2. making bonds to 4 DIFFERENTthings Chapter 5a: Biological Molecules (polymers,carbohydrates,lipids) BiologicalMolecules • Synthesis of polymers frommonomers ○ Dehydrationandhydrolysis reactions • Classes of biological molecules: 1. Carbohydrates 2. Fats 3. Proteins 4. Nucleic Acid • For eachbio molecules shouldknow: ○ Name of the monomer ○ Generic monomerstructure ○ Type of bond and how formed ○ Polymer structure ○ Examples of molecules ○ Examples of roles of eachmolecule ○ Molecule-specific info abouteach Polymers • Macromolecules(large molecules) are polymers:longchains of similar subunits ○ Eachsubunit=monomer • Polymers are assembledbythe same chemical mechanism,a dehydrationreaction ○ Dehydrationreaction:ahydroxyl groupandhydrogenare replacedbya covalentbond,producinga polymer,releasing water • All macromoleculesare assembledbythis basic reaction: ○ Dehydrationreaction:ahydroxyl groupandhydrogenare replacedbya covalentbond,producinga polymer,releasing water • All macromoleculesare assembledbythis basic reaction: • Hydrolysis is opposite of dehydration ○ Water molecule replacesacovalentbond,adding a hydroxyl to one and a hydrogen to the other. • Macromoleculesare brokendownthroughhydrolysis,inthe cell or elsewhere Carbohydrates • Carbohydrates:sugars andpolysaccharides ○ Name derivedfromcarbon-hydrate (equal amounts of carbon and water) general structure= Cn (H2O)n where n=3, 5, or 6 • Types ofcarbohydrates: ○ Sugars § Monosaccharides:monomer that others are basedon (AKAsimple sugar) § Disaccharides;2monosaccharides together bythe dehydration method ○ Polysaccharides § Starch,cellulose,chitin • Monosaccharides ○ Commonly 3, 5, or 6 carbons ○ Structure:1carbonyl groupremainingCbonds to -OH and -H ○ Sugar families namedaccordingto # of carbons: ○ Polysaccharides § Starch,cellulose,chitin • Monosaccharides Commonly3, 5, or 6 carbons ○ ○ Structure:1carbonyl groupremainingCbonds to -OH and -H ○ Sugar families namedaccordingto # of carbons: § 3 C = triose § 5 C = pentose § 6 C = hexose ○ 2 families basedon carbonyl position § Aldoses:carbonyl is terminal C § Ketoses: carbonyl is internal C • Sugar Isomers ○ Arrangement of-H and-OH at a single asymmetric carbon causes differentproperties § Glucose andgalactose are enantiomers ○ • Ring Sugars ○ Pentose's are hexoses spontaneouslycircularize to rings (linear formshownbefore is rare) ○ Shorthanddepictionof sugar structure: § Eachcorner is a Catom § Thicker edge is towardthe reader ○ When sugars formrings,the carbonatominthe reaction(C# ○ When sugars formrings,the carbonatominthe reaction(C# 1) is an asymmetric carbonandthus 2 differentenantiomers are possible § A- Glucose andB-Glucose § • Disaccharides ○ Two monosaccharides joinedbyadehydrationreaction § Glycosidic linkage=covalentbondbetweentwo sugars § Monosaccharidecomponents andbondposition determine disaccharideidentity □ Sucrose =glucose +fructose □ Maltose =glucose +glucose § C6H12O6=C12H22O11 • Polysaccharides Generallynotsweet ○ ○ Multiple monosaccharides joinedinapolymer § 100s to 1000s monomers § Glycosidic linkages § Unbranchedor branched § Properties determinedbymonosaccharide monomers and bond type ○ Polysaccharideswithdifferentpropertiesare made fromA- and B- monomers ○ ○ The differenceis starchuses alphamonomers andcellulose uses betamonomers. ○ The differenceis starchuses alphamonomers andcellulose uses betamonomers. ○ Examples: § Starch,glycogen(carbohydrate storageinplants, animals) § Cellulose (plantstructure) § Chitin (fungalcell wall, insectexoskeleton,dissolving surgical thread) • Artificial Sweeteners ○ Artificial sweeteners mimic the structure of sugars ○ Ex: Splenda, a disaccharide-likemolecule.Note the chlorine atoms in place of hydroxyls-these prevent breakdown by the body, so no calories ○ Chlorine canformcovalentbonds (as inSplenda) or ionic bonds (as in NaCl) ○ • Clicker Question ○ Why are carbohydrates soluble inwater? § Manypolar bonds Lipids • Types of Lipids 1. Fats and oils 2. Phospholipids 3. Steroids ○ Notreallypolymers or macromolecules ○ Commonproperty:Hydrophobic (notsolubleinwater) 1. Fats and Oils ○ Function:storage molecules ○ Structure:glycerolandfattyacids § Glycerol:3-carbonalcohol § Fatty Acid:linear hydrocarbonwithterminal carboxyl □ Mostcommonhave16 or 18 carbons □ Have a acidat the end ○ Structure:glycerolandfattyacids § Glycerol:3-carbonalcohol § Fatty Acid:linear hydrocarbonwithterminal carboxyl □ Mostcommonhave16 or 18 carbons □ Have a acidat the end § ○ Synthesis:Fatty acids are joinedto glycerol bya dehydration reaction ○ TYPES § Triacylglycerol:3fattyacids attached to glycerol □ All fatty acids may be the same (below) □ Fatty acids may be different,dependingonwhat kindof fattyacids it contains □ § Saturated and Unsaturated □ Fatty acids may have all single bonds or some double bonds ® All single bonds: hydrocarbon chain is straight ◊ Fats with ALL single bond fatty acids=saturated fats ◊ More hydrogens, saturating the fatty acids with hydrogens ◊ Saturates fats pack together tights= high melting point } Solid at room temp } Animal and some plant storage ® Some double bonds: hydrocarbon chain is bent ◊ Oils with some double bond fatty acids=unsaturated fats ◊ Carbon Carbon double bond ◊ Unsaturated fats do not pack because of kink in } Animal and some plant storage ® Some double bonds: hydrocarbon chain is bent ◊ Oils with some double bond fatty acids=unsaturated fats ◊ Carbon Carbon double bond ◊ Unsaturated fats do not pack because of kink in hydrocarbon chain= low melting point } Liquid at room temp= "oil" } Most plant storage fats § Phospholipids □ Function: Major component of membranes. Not energy storage. □ Structure: ® 2 fatty acids attached to glycerol. FA's can be same or different, saturated or unsaturated ® 3rd glycerol carbon attached to phosphate and to a small polar molecule. (Choline in figure) ® Presence of both hydrophobic and hydrophilic regions is important for membrane structure. § Steroids □ Structure: basic structure is four attached rings ® Examples: cholesterol (shown), estrogen, testosterone, cortisol, anabolic steroids, etc ® Different steroids differ in chemical groups attached to basic 4-ring structure □ Function: ® Hormones ® Membrane component (cholesterol) Chapter 5b: Macromolecules (proteins and nucleic acids) Proteins • Ubiquitous and divers. 50% mass of cells • Functions (most of the rest of course) ○ Enzymes ○ Structure ○ Transport ○ Movement ○ DNA synthesis ○ Transcription, translation and regulation ○ ETC. • Monomers/Amino acid ○ Polymer=protein (AKA "polypeptide") ○ Monomer=amino acid ○ Transcription, translation and regulation ○ ETC. • Monomers/Amino acid ○ Polymer=protein (AKA "polypeptide") ○ Monomer=amino acid ○ Amino acid structure: § Amino group-alpha carbon- carboxyl group ○ A-Carbon also attached to -H and to an "R" group § R (aka "side chain")= 20 different chemical groups ○ The 20 common amino acids.-groups in colors according to chemical properties ○ The properties of amino acids are defined by the propertier Rf thei- groups § ○ Polar groups: § ○ Charged amino acids § ○ Synthesis § Amino acids joined by dehydration reaction between amino and carboxyl groups § Bond=Peptide Bond § Polymer (polypeptide) □ Unbranched □ Backbone=repeating ® N-C-C -N-C-C -N-C-C - …….. □ Side chains extend from back backbone (R -Groups) • Structure: 1. Primary structure= order of amino acids in polypeptide □ Determined by instructions in a gene □ Range of polypeptide lengths: tens to thousands of amino acids □ Because of the amino-to-carboxyl nature of the peptide bond, one end of the peptide has an exposed amino group, and the other a carboxyl group= N-Terminus or Amino Terand s C-Terminus or Carboxy-lTerminus □ 2. Secondary Structure= local interactions, dbonds between > N-H and >C=O groups in the polypeptide backbone □ 2 common secondary structures, present in many different proteins: ® A-helix: backbone makes a spiral ◊ A-Helix held together by hydrogen bonds between carbonyl and amino groups of every 4th amino acid in the helix ® B-Pleated sheet- backbone makes waves, or pleats ◊ B-Pleated sheets lie adjacent and form a sheet. ® A-helix: backbone makes a spiral ◊ A-Helix held together by hydrogen bonds between carbonyl and amino groups of every 4th amino acid in the helix ® B-Pleated sheet- backbone makes waves, or pleats ◊ B-Pleated sheets lie adjacent and form a sheet. Adjacent strands aligned by H -Bonds □ 3. Tertiary Structu= overall, l-scale 3D structure, interactions between amino acid R-Groups ® Ex: Lysozyme (antibacterial component of egg whites) □ Compact, roughly spherical proteins (Lysozyme) = Globular □ Extended, roughly linear proteins (Coll= rous • Structure-Secondary and Tertiary-Protein Folding ○ Secondary and tertiary structure: What determines how proteins fold? § Chemical interactions between amino acids: □ Hydrogen bonds between C=O and N-H group in the backbone □ Various Interactions between R -Groups: ® Ionic and hydrogen bonds and Van der Waals interactions ® Hydrophobic interactions ◊ Water makes H-Bonds with polar and charged amino acid side chains.-polar (hydrophobic) R-groups fold to the internal, non-aqueous portion of the protein ® Disulfide bridges ◊ Two cysteine amino acids adjacent through folding form a covalent bond. ◊ Cysteine R-group is -CH2-S-H ◊ Two Cysteine's: } -CH2-S-H H-S--CH re linked by a covalent bond- CH2-S - S-CH2-+ H2 = Disulfide bond § The function of some proteins is to help other proteins fold § Helper proteins haperonins § Complex mechanism (omit) • Structure: 1. Quaternary Structure= functional protein composed of >1 polypeptide. Many but not all proteins § The function of some proteins is to help other proteins fold § Helper proteins haperonins § Complex mechanism (omit) • Structure: 1. Quaternary Structure= functional protein composed of >1 polypeptide. Many but not all proteins □ Examples: collage (3 polypeptides intertwined). Hemoglobin: 2 molecules of a -globin + 2 molecules of B-globin □ Hydrogen bonds, ionic bonds, Van der Waals, hydrophobic interactions, disulfide bonds 2. Most genetic diseases are caused by mutations in genes that result in an altered amino acid sequence □ Example: sickle cell disease. Amino Acid 6 of hemoglobin changed from Glu to Val (glutamic acid to valine) □ Causes change in protein folding, assembly into fibers, misshapen red blood cells with lower O2 capacity □ Abnormal red blood cells get stuck in capillary=sickle cell disease Nucleic Acids • Monomer= Nucleotide ○ Components of a nucleotide: § Phosphate § Sugar § Base • Polymer= Polynucleotide ○ Examples: DNA and RNA • Nucleotide Structure: Phosphate and Ribose sugars ○ § Phosphate: -PO4 § Sugar: Pentose □ Typical Pentose sugar § Deoxyribose in DNA □ Atypical - has 2 H's on C #2 rather than 1 H and 1 OH ○ Phosphate and Ribose sugars § Phosphate: -PO4 § Sugar: Pentose □ Typical Pentose sugar § Deoxyribose in DNA □ Atypical - has 2 H's on C #2 rather than 1 H and 1 OH ○ Nitrogenous bases § Nitrogenous bases. Two Families: 1. Pyrimidines: single rings. 4Cs and 2Ns in ring. Different functional groups 2. Purines: Double ring. 5Cs and 4Ns in rings. Different functional groups. • Nucleotides ○ Nucleotides are the monomers for DNA and RNA ○ Nucleotides are the energy -containing and regulatory molecules ATP and GTP • Polymers-DNA and RNA ○ Nucleotides linked together in polymers: § Sugar-phosphate-sugar-phosphate backbone with bases sticking out Atomic formulas of Biological Molecules Water (60% of body by weight) H20 Carbohydrates (glucose) C6H12O6 Lipid (saturated fatty acid) C18H36O2 Protein (amino acid alanine) C3N1H7O2 Atomic formulas of Biological Molecules Water (60% of body by weight) H20 Carbohydrates (glucose) C6H12O6 Lipid (saturated fatty acid) C18H36O2 Protein (amino acid alanine) C3N1H7O2 Nucleic Acids (nucleotide ATP) C10H15O13N5P3 Chapter 6: Tour of the cell A. Membrane-Bound organelles Basics of Cell structure • All cells have membranes • Membrane: barrier to passage of most molecules. Selective, regulated permeability • Structure/function in topic #7 • Plasma membrane: encloses the entire cell. All cells have PM • Cytoplasm:everything inside the plasma membrane Organismal classification based on cell type • Fundamental division of living organisms, eukaryotes, prokaryotes and archaea, is based on cell structure. ○ Eukaryotes: "true kernel" Have a nucleus and other organelles § "Kernel"=Nucleus § Euks= Animals, plants, fungi, true algae, protists ○ Prokaryotes: "Pre-Kernel" § Bacteria (blue-green algae) § archaea • Which pair of organisms is most closely related? ○ Human-Mushrooms ○ Humans and mushrooms are both eukaryotes • Eukaryotic Cells ○ All cells have an external membrane, the plasma membrane ○ Eukaryotic cells also contain internal m-eound organelles ○ Organelle: membrane-enclosed structures Membrane-Bound organelles • Nucleus: ○ Function: contains genes and necessary enzymes and regulatory molecules, etc. ○ Structure: membrane= Nuclear envelope Membrane-Bound organelles • Nucleus: ○ Function: contains genes and necessary enzymes and regulatory molecules, etc. ○ Structure: membrane= Nuclear envelope § Double membrane. Outer membrane continuous with endoplasmic reticulum § Inner and outer membranes are fused in some locations, forming "holes" or nuclear pores (where the inner and outer membrane connect) § Nuclear Lamina : network of fibers on inside of inner membrane ○ Inside the nucleus: § Chromosomes:structures that contain genes § Chromosomes are made of Chromatin:DNA plus proteins § (Chromosome and chromatin structure = topic 16) • Some cells produce proteins that end up outside the cell [eg., pancreas (digestive enzymes, insulin), pituitary (many hormones)]. How do these proteins get out of the cells that make them? ○ Membrane-bound vesicles that contain 33% the proteins fuse with the plasma membrane. • Endomembrane system: network of vesicles (vesicle: small membrane "sac") ○ Functions: Protein synthesis and metabolic functions ○ Components: 1. Smooth endoplasmic reticulum (sER) □ Structure: network of vesicles and tubes, usually close to nucleus ® Lumen: interior of vesicle □ Function:Metabolic. Enzymes are concentrated in lumen ® Lipid synthesis: membrane lipids, steroid hormones, etc. ® Carbohydrate metabolism ® Detoxification of drugs and other "foreign" chemicals 2. Rough endoplasmic reticulum (rER) □ Structure: ® Layers of flattened sacs ® Quantity varies depending on cell type ® Ribosomes attached to outer surface (roughness=ribosomes) □ Digression: Ribosomes ® Function: protein synthesis ◊ Ribosomes on rER membrane synthesized proteins that pass thru a pore into rER lumen In rER lumen, proteins fold into 3D shapes and (roughness=ribosomes) □ Digression: Ribosomes ® Function: protein synthesis ◊ Ribosomes on rER membrane synthesized proteins that pass thru a pore into rER lumen ◊ In rER lumen, proteins fold into 3D shapes and carbohydrates are added ® Complex of protein and RNA ® Location: Cytoplasm ◊ "Bound" Ribosomes:attached to outer surface of rER ◊ "Free" Ribosomes:not attached to the ER } Do not end up outside of the cell, make proteins that are inside the cell ® Pathway: ◊ rER is 1st stage o ecretory pathway and related pathways ◊ Goal: synthesize, process and sort proteins for export from cel(ecretion) and other destinations within cell (lysosomes, vacuoles) ◊ The secretory pathway: 1. rER: synthesis, procession 2. Golgi apparatu: processing, sorting 3. Plasma membrane: secretion ◊ Transitions in the stages a:ransport vesicles carry proteins from rER to Golgi, between Golgi stacks, from Golgi to plasma membrane, etc. □ Proteins synthesized in rER: ◊ Secreted proteins (outside the cell) ◊ Plasma membrane proteins ◊ Proteins destined for various endomembrane compartments (sER, rER, Golgi, lysosomes) □ rER quantity varies by cell type: ◊ Cells in glands have a lot of rER to produce secreted enzymes/hormones (pancreas, salivary, adrenal) 3. Golgi apparatus □ Structure: flattened stacks of vesicles, more compact, less extensive than ER ® Transport vesicles bud from rER, fusci sface of Golgi stack ® Transport vesicles carry from one level of Golgi to next ® Transport vesicles leave fransface to plasma extensive than ER ® Transport vesicles bud from rER, fusci sface of Golgi stack ® Transport vesicles carry from one level of Golgi to next ® Transport vesicles leave fransface to plasma membrane, lysosomes and vacuoles ® Cis: near Trans:away from □ Functions: ® Processing: ◊ More carbohydrates added to proteins ® Sorting: ◊ Contents are sorted and marked for destinations: } Cell surface (secretion/exocytosis) } Lysosomes (digestive enzymes) } Various vacuoles 4. Transport vesicles 5. Lysosomes □ Structure: spherical organelles □ Function: digestion of endocytosed particles and worn-out organelles ® Some cells engulf other cells via phagocytosis (cell eating). Internalized food vacuoles fuse with lysosomes for digestion ® Damaged organelles are enclosed by vesicles, which fuse with lysosomes for digestions ( autophagy) □ Lysosomal digestive enzymes are routed to lysosomes via rER and Golgi 6. Vacuoles □ Various functions and structures: ® Contractile vacuoles pump excess water from cell (freshwater protozoans) ® Food vacuole: product of phagocytosis ® Central vacuole: mostly storage (plant cells) ® Fat storage vacuoles in adipose tissues ® Etc. § Peroxisomes □ Structure: roughly spherical with granular/crystalline core □ Function: ® Detoxification of alchol and poisons, breakdown of drugs, etc. (liver) ® Breakdown of fatty acids ® Detox reactions remove hydrogens from drugs to produce H2O2 (hydrogen peroxide, thus name) Methods ® Detoxification of alchol and poisons, breakdown of drugs, etc. (liver) ® Breakdown of fatty acids ® Detox reactions remove hydrogens from drugs to produce H2O2 (hydrogen peroxide, thus name) Methods • Light microscopy ○ Advantages § Many specimen prep methods are simple. § Can be used on living cells § Methods to detect specific molecules § Variations to enhance contrast ○ Disadvantages § Most organelles too small § Resolution is limited to .2um (physical property of light), although computer process can partially circumvent this limit • Electron microscopy ○ Advantages § High resolution (2 nm), enough to see organelles ○ Disadvantages § Not for living specimens § Complex specimen preparation § Difficult methods to detect positions of specific molecules • Cell fractionation ○ Goal: purify organelles based on size or density 1. Homogenized (gently grind up) cells 2. Centrifuge at low speed, to produce a pellet and supernatant 3. Centrifuge at higher speed 4. Centrifuge at even high speed, etc. Chapter 6: A tour of the cell B: The cytoskeleton, extracellular components The cytoskeleton • "skeleton" and "muscles" of the cell. Necessary for strength/rigidity and force/motility • Three components: 1. Microtubules § Composition: hollow tube composed of protein tubulin The cytoskeleton • "skeleton" and "muscles" of the cell. Necessary for strength/rigidity and force/motility • Three components: 1. Microtubules § Composition: hollow tube composed of protein tubulin □ Tubulin: dimer of-tubulin and b-tubulin § Position within the cell: internal, appear to radiate from a central point, the centrosome § Function: rigidity, strength, organelle movements § Motor proteins move along MTs, using energy from ATP hydrolysis § Can move attached organelles or slide MTs past each other § MT-based structures: □ Cilia: short and many □ Flagella: long and few (usually 1 or 2) § Structure: cytoplasmic extension containing complex arrangement of MTs § Bending results from MTs sliding past each other, driven by motor protein dynein 2. Microfilaments (AKA actin filaments) § Composition: rod composed of globular protein actin (AKA "actin filaments") § Position within the cell : usually peripheral § Function: cell motility and structural □ Reinforce microvilli □ Amoeboid movement □ Cytoplasmic streaming □ Muscle contraction (muscle cells) § Motor: myosin 3. Intermediate filaments § Composition: rope-like filaments compose of fibrous proteins § Not found in all cell types limited to vertebras § Position within the cell: Internal, throughout § Function: strictly structural § Motors:None. No function in movement § Also extracellular (skin, hair, nails, feather, etc. composed of keratin.) • Plants and animals differ dramatically in their ability to move. Why? ○ Plant cells are surrounded by rigid cell walls and animal cells are not Extracellular Components • Extracellular components: structures formed outside the cell (external to plasma membrane) 1. Cell Wall (plants, fungi, algae) ○ Extracellular Components • Extracellular components: structures formed outside the cell (external to plasma membrane) 1. Cell Wall (plants, fungi, algae) § Provides the main structural feature of plants § Components: celluloseand other polysaccharides, proteins and glycoproteins § Glycoproteins:proteins with attached polysaccharides § Components secreted by cells into extracellular space via the secretory pathway 2. Extracellular Matrix (animals, protozoans) § Animal cells § Structure: interlocked extracellular fibers, made of proteins, polysaccharides, glycoproteins, etc. □ Collagen (most abundant ECM protein). Also fibronectin and proteoglycans □ Cells another to ECM proteins through integrinproteins § Synthesis: components secreted via secretory pathway § Function:mechanical strength. Cell-cell communication § In some tissues, ECM >> cells. Examples: □ Tendons and ligaments □ Bone and cartilage □ Teeth □ Etc. Cell Junctions • Cell junctions: connections between cells ○ Cell-cell connections in plants § Plasmodesmata: Holes in cell wall. Membranes of adjacent cells are continuous and cytoplasm is in contact □ Cytoplasmic extensions connecting the cells □ Can exchange molecules, how they communicate with eachother ○ Cell-cell connections in animals § 3 types of junction: 1. Tight Junction:specialization connects membranes of adjacent cells ® Acts as barrier to passage of fluid between adjacent cells ◊ Ex: intestine, blood vessels. Contents in the lumen cannot ooze between cells ◊ Important to line the hollow tubes of cells with liquids passing ® Acts as barrier to passage of fluid between adjacent cells ◊ Ex: intestine, blood vessels. Contents in the lumen cannot ooze between cells ◊ Important to line the hollow tubes of cells with liquids passing ◊ 2. Densomes:mechanical cell-cell attachments, reinforced w/ intermediate filaments ® Example: Skin 3. Gap Junctions:cytoplasmic continuity between adjacent cells, passage of molecules ® Equivalent in function to Plasmodesmata ® Passage of molecules from the cytoplasm of one cell to the cytoplasm of another cell Chapter 7: Membranes Membrane Structure • Membranes separate external from internal, and subdivide cytoplasm into organelles Cell contents and external environments are aqueous. Membranes form a ○ hydrophobic barrier between inside and outside ○ Purpose: concentration and regulation of biological chemistry, and compartmentalization of function • Position of two components are accounted for by the Fluid Mosaic Model: 1. The lipid bilayer § Phospholipid Structure: □ Fatty acid tails (hydrophobic) □ Polar "head" (hydrophilic) □ Amphipathic: Molecules with both hydrophobic and hydrophilic regions § Other membrane lipids are also amphipathic: Cholesterol, glycolipids (lipids with carbohydrates attached), etc. □ Fatty acid tails (hydrophobic) □ Polar "head" (hydrophilic) □ Amphipathic: Molecules with both hydrophobic and hydrophilic regions § Other membrane lipids are also amphipathic: Cholesterol, glycolipids (lipids with carbohydrates attached), etc. § Lipid Bila: double layer of lipids □ Polar head groups on the periphery make H - Bonds and ionic bonds with water and other hydrophobic molecules □ Fatty acid tails internal form an internal hydrophobic "core" □ □ □ All membranes have this structure 2. Proteins A. Integral membrane proteins : "float" like icebergs in a 2D sea of lipids □ Most are transmembrane proteinthat span the lipid bilayer □ Hydrophobic regions of proteins are embedded in the core of the bilayer □ Hydrophilic parts are exposed on either side □ Most integral membrane proteins span the bilayer multiple times ® Membrane-spanning parts are usually a -helics with hydrophobic amino acids ® Hydrophilic amino acion the cytoplasmic and extracellular faces ® Ex: junction proteins extracellular faces ® Ex: junction proteins ® □ Integral membrane proteins are more or less free to move in the lipid bilayer □ Experiment: membrane proteins are labeled with dyes, one color for each cell ® Cells are fused. Membrane proteins move in the hybrid cell bilayer, eventually become mixed and unifrom B. Peripheral membrane proteins : Not embedded in the membrane. Attached by covalent or non -covalent bonds to: □ Lipid head groups □ Integral proteins □ Other peripheral proteins (not embedded in the lipid bilayer) C. Membrane Fluidity: degree to which lipids and proteins move in the plane of the membrane □ Fluidity varies with temperature (higher fluidity at higher temp) □ Also fluidity varies with lipid composition: ® Many unsaturated phospholipids= high fluidity ® Many saturated phospholipids= viscous (low fluidity) □ Organisms adjust to temperature changes by varying membrane lipid composition Membrane Function • Permeability of the lipid bilayer ○ Movement of molecules across the lipid bilayer (no proteins): § Cross easily: non-polar molecules (CO2, O2, steroid hormones) § Cross slowly: small polar molecules (H20) § Do not cross: larger polar, or charged molecules of any size (ions, sugars, amino acids, etc.) • Diffusion ○ Diffusion: spreading of a molecule in available space ○ Molecules move spontaneously from high to low concentration, (down a concentration graditn) ○ Equilibrium: no net movement = equal concentration everywhere • Diffusion ○ Diffusion: spreading of a molecule in available space Molecules move spontaneously from high to low concentration, (down a ○ concentration graditn) ○ Equilibrium: no net movement = equal concentration everywhere ○ ○ Example: sugar dissolved in a cup of water § Sugar concentration is high at the bottom of the cup, lower at the top. Water concentration is high in the top part of the cup, lower at the bottom § Eventually the sugar and water concentrations become uniform, through diffusion • Osmosis ○ Osmosis:Diffusion of water across a membrane. A special case of diffusion ○ Relevance to biology: water can cross lipid bilayers but dissolved chemicals (salts, sugars, etc.) cannot ○ Illustration of osmosis: two sugar solutions by a membrane. Membrane allows water to cross, but not sugar § Left: Low (sugar) = high (water) § Right: High (sugar) = low (water) ○ Sugar cannot cross, but water moves from high to low concentration. Volume on right side increases to accommodate increases H2O ○ The plasma membrane of cells (and other membranes) ismi se- permeable membrane § Allows the passage of water § Prevents the passage of most solutes ○ The plasma membrane of cells (and other membranes) ismi se- permeable membrane § Allows the passage of water § Prevents the passage of most solutes ○ Solvent: liquid in which solute is dissolve (in bio=water) ○ Solute: molecule dissolved in a solvent ○ Compare external solute concentration, relative to internal (inside the cell) ○ Hypotonic § External solute concentration is lower than that of cell. External water concentration is higher § Result: water rushes into cell (high concentration to lower concentration). Animal swells and explodes. § Rigid cell walls limit cell expansion (plant, fungi bacteria) § Osmoregulation example: Paramecium (fresh water protozoan, no cell wall). Water is collected in contractile vacuole, which expels water by concentration § ○ Hypertonic § External solute concentration is higher that internal. External concentration is lower than internal. § Result: cells lose water and become shriveled (upper and lower) § Happens to both animal cell and plant cell (separate from cell wall) § Osmoregulation example: ocean fish and birds must excrete salt to avoid become hypertonic § § ○ Isotonic § Isotonic: solute concentration same as that inside the cell § Result: No movement of water. Red Blood Cell remains the same size (animal cell) § Animals maintain internal fluids that are isotonic with cells § • Membrane Transport ○ Passive Transport: molecule moves from higher to lower concentration § Diffusion:Molecule crosses membrane without assistance. (O2, CO2 into lung cells, water) § Facilitated diffusion: Large polar or charge molecules cannot cross lipid bilayers. (Ions, sugars, amino acids) § Facilitate diffusion requires transporter proteins: □ Channels: hydrophilic channel on inside of protein □ Carriers: hydrophilic space changes shape, alternately § Facilitate diffusion requires transporter proteins: □ Channels: hydrophilic channel on inside of protein □ Carriers: hydrophilic space changes shape, alternately exposed to inside and outside of membrane § Facilitated diffusion is always gated(pores can be closed and opened) § Water crosses the plasma membrane by diffusion and sometimes by facilitated diffusion □ Diffusion: leaks through the lipid bilayer □ Facilitated diffusion: through channels called aquaporin's ® Ex: plants (to maintain turgor), kidney cells (reclaiming water from urine) ○ Active Transport: movement of a solute across a membrane against its concentration gradient (from lower to higher concentration) § 2 forms of active transport: □ ATP-Driven ® Ex: sodium-potassium pump. Maintains low intracellular sodium, high intracellular potassium ◊ Uses energy obtained by breaking bonds of ATP (=" ATP Hydrolysis") to cycle pump ◊ Pumps NA+ out of and K+ into cell □ Co-Transport:movement of one solute down its concentration gradient provides the energy to move another up its concentration gradient ® Ex: Sucrose Transport. Movement of H+ ions down its concentration gradient drives movement of sucrose against its concentration gradient • Bulk transport ○ Exocytosis and endocytosis: specialized processes for bulk movement into and out of cells, respectively. ® Ex: Sucrose Transport. Movement of H+ ions down its concentration gradient drives movement of sucrose against its concentration gradient • Bulk transport ○ Exocytosis and endocytosis: specialized processes for bulk movement into and out of cells, respectively. ○ Exocytosis:small membrane-bound vesicles fuse with the plasma membrane. Contents of vesicle are delivered to outside of cell § Last step in t ecretory pathway § ○ Endocytosis:cell "engulfs" nearby parts of environment, forming a new internal ve
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