Cell Molecular Bil
Cell Molecular Bil BIL 255
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This 20 page Class Notes was uploaded by Quinten Beatty on Thursday September 17, 2015. The Class Notes belongs to BIL 255 at University of Miami taught by C. Mallery in Fall. Since its upload, it has received 14 views. For similar materials see /class/205741/bil-255-university-of-miami in Biology at University of Miami.
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Date Created: 09/17/15
Bil 255 Mallery Bil 255 CMB Chemical Makeup of Living Cells Mallery Molecules quells Molecules of Cells Molecules of Living SysTems chapTer 2 pg 2950 T e chemical properTies of The living sTaTe The sTrLIcTLIre of biological molecules how Their shape deTermines The roles They play in The complex chemical processes of life Even The mosT complicaTed biological molecules can be divided inTo smaller and smaller funcTional groups REDUCTIONISM Some Web Resources that give 3D shapes of Biomolecules A Site ofthe Molecules of Life mwk Mallery Molecules of Cells 2 The chemicals of life nTical number of p ELEMENTS subsTances composed of aToms all having an ide roTons can39T be reduced To simpler subsTances by normal chemical means only 30 of 92 elements OCCUR IN LIVING SYSTEMS 99 of LIVING MATTER is made ofC H O N P 5 all have low atomic numbers d are easily reacTive d form covalenT bond Molecular composition of cells o WaterH Inorganic ions Na K Cl P04 Small molecules aa s sugar nucle Macromolecules protein na etc Mallery Molecules of Cells Biomolecules Weak Forces amp Design of MeTabolism 1 BIOMOLECULES carbon skeleTons mosle carbon compounds are found in living sysTems W Carb easily forms 4 covalenT bonds Thus makes many small biomolecLIles allows 3D shapes ThaT can evoke biological acTiviTy possesses greaT chemical reactivit inTeracTs wiTh common chemical funcTional groups o 3 v Functional Groups groups of atoms acts as a unit give organic molecules their physical properties chemical reactivity amp solubility in aqueous solutions c mon functional rou squot In biomolecular chemistry the concept offunctional groups is useful as a basis for 39 39 39 3 UI r 39 to their chemical properties and react ty most groups possess electronegatlve atoms 0 N P 51 key bonds are ester C C amp amide C most are ionizable at phy ological pH 68 to 74 read pages 4050 Mallery Molecules of Cells 4 Mallery Bil 255 2 small Biomolecules monomers Four majors groups of small biomolecules a SUGARS compounds with formula CH 20 quot aldoses vs ketosesquot rings g amp Blinksquot isomers glucose vs galactosequot glucose glucose mono disaccquot tri at long chain polymers of monosacch b FATTY ACIDS long chain hydrocarbons saturated vs unsaturatedquot m lipidsquot trlacylglyce l and phospholipidsquot poly saccharidesquot E arides ro animal fats of membranes easily selfassembly into gggregatesquot soap micelle bilayers steroid d cholesterolsquot 4ring skeleton are lipids because they39re insoluble Mallery Molecules of Cells Structural Chemistry orientation of covalent bonds in space molecular con gura ion results in speci c bond angles and molecular geometry methane CH4 10950 atetrahedron with 39ee rotation formaldehyde H2CO 1200 same plane with no 39ee rotation one key to shape is the ASSYMETRIC CARBON a car on atom bound to 4 ssimilar atoms 39 nonplanar con guration tetrathedron results in 2 different spatial orientations producing CHIRAL molecules ones that are mirror images of each other optical or stereoisomers Mallery Molecules of Cells Molecules of Cells C AMINO ACIDSquot Fig 2 21 peptide bo d hundreds known but only 20 common in proteins of cell once established in the quot rimordial cel quot certain small biomolecules as covalent e seem to have been preserved th me throughout evoluti n Ie they were favored energetically d NUCLEOTIDESquot parts nitrogen containing quotringquot compounds a nitrogenousbase linked to a 5carbon sugar 39 ose amp deoxyribose amp a phosphate pyrimidines C T U purines A G nucleotides form the energy rich compounds 1 cells as ATP ampGTP as well as the nucleic acids Mallery Molecules of Cells ENANTIOMER molecules that are nonsuperimposable mirror images of one another called Stereoisomers two molecules are not equivalent or identical and have 2 molecular orientations or mirror images an optically active CHIRALquot is not superimposable on its mirror image c Iral animation stereoisomers may have mostly identical chemical properties to en rotate plane of polarized light via di an les LEVOROTARYquot L rotate Iig elt negative optical rotation DEXTRORTATORY D rotate light right positive optical rotation and likely have different BIOLOGICAL ACTIVITY Parkinson39s Disease amp dihydroxyphenylalanine LDOPA fgurequot Mallery Molecules of Cells Bil 255 Mallery Molecules of Cells Biological Activity amp the Shapes of Biomolecules Biological activity is catalytic ability of molecules to do work There are 2 rop rties of biomolecules which ives the their unique FITNESS for Biological Activity 4 the Living State A CONFIGURATION the spatial arrangement of atoms in molecules configuration can39t be interconverted wo bredlting bonds based upon COVALENT BONDquot sharing of outa orbital e39s between two atoms thereby forming a molecule examples of Covalent Configurations isomers based upon covalent bond configurations qu v gal quot Mallery Mulecules quells a BIOLOGICAL ACTIVITY amp the Shape of Biomolecules B CONFORMATION or shape surface outline or contour or D orientation of chemical groups that are free to assume different positions in space without breaking any bonds to do primarily to ROTATION of atoms about a single chemical bond WEAK NONCOVALENT FORCES hold atoms in spatial arrays consequences of conformations 39 erent isomeric shapes forms of molecules can exist only one of which may be biologically active others aren39t ENZYMES can distinguish between biologically active forms isomers based upon the quotSHAPEquot of that isomer Mallery Mulecules of Cells in Weak Molecular Forces of Life see Panel 27 pg 78 Noncovalent Electrostatic lnteractionsquot in the 10150 calmoi waftr on atom Mallery Mulecules of Cells ll Covalent Molecular Forces of Life see table 21 pg 46 TYPE of BOND ENERGY Kcmoi TYPE of INTERACTIONS ENERGY Kcmoi SINGLE COVALENT BONDS NONCOVALENT BONDS O H 110 IONIC BONDS 10 50 H H 104 HYDROGEN BONDS 10 20 C H 99 VANDER WAALS 01 10 C O 84 HYDROPHOBIC 0 10 C C 83 S H 81 C N 70 C S 62 DOUBLE BONDS C O 170 C N 147 C C 146 Mallery Molecules of Cells 12 Bil 255 Mallery Biological Design or39 How Weak Molecular Forces 6t Shape Build Form Is there runaameniui Erinci ie guides biological nr garilzclllnn in Erclcllce 7 some cummnnrunlverscll rules or molecular assembly musl exisl one sees recurring pallerns or spirals lrlangulalzd rarms a pentoaans in ever hing from crystals to protons ses to plankton peremecie to protozoa Tenseg tys is an architectural principle or biological shape a form How inaiyiaual groups or molecules assemble themselves Within whale iiying organisms is a runaameniai quesllnn or the iiying cundlllnn m nsiiery noiecuiesoiceiis is Molecules of Cells PRINCIPLE of SELFASSEMBLY molecules join to form larger a more stable structures often with news nonpredicted properties or emergent properties macromolecules gt organelles gt cells gt tissues gt organs The answer may lie in the principles of fensegrify the application or general architectural principles to biomolecules a living systems rinsmuw defines the mechanical rules and how structures are stabilizede balancing forces of internal tension and compression nsiiery noiecuiesotceiis M TENSEGRITY may be a fundamental aspect of SELFASSEMBLY an architectural system mechanically stable yet dynamic where the forces of tension and compression balance Geodesic Domes Prestress Sli39u ui es Buckminster Fuller Snelson ic entire structure distributes its SW15 that beartenmon mechanical stresses are distinct from ones tnat bear compression ira co oentagons or 9 Compression members can each or n h provide rigidity while remaining compregslo separate not toucning one another eid in stasis only by m a s or tense ires in both e n oitnese structures tension is continuously transmitted across all structural members nsiiery noiecuiesoiceiis is Tznsegr ify in Biological Sysfz chlieciure of Life by Don Ingber organisml Level examples bones are the compression struts and muscles tendons a ligaments are the tension bearing wires Call 197039s view membrane bound viscous gel molasses filled balloon today toskeletal awash in aviscous gel elements is microtubules act in compression r quot and microfilaments exert tension pulling all a cells parts toward nucleus cytoskeleton is then a hardwired molecular system that stabilize cell form a shape nsiiery noiecuiesotceiis is Bil 255 Mallery Molecules of Cells Biological TensegriTy suggesTs ThaT The sTrucTure of cell39s cyToskeleTon can be changed by alTering The balance of physical forces TransmiTTed across The cell39s surfaces for example culTured cells on glass flaT vs a flexible surface round Donald Ingber39s TenseqriTy Model of aCell TensegriTy furTher suggesTs Since many enzymes and oTher subsTances ThaT conTrol proTein synThesis energy conversion at growTh in The cell are physically immobilized upon The cyToskeleTon changing The cyToskeleTal geomeTry d mechanics may affecT biochemical reacTions at even alTer The genes which are acTivaTed and Thus The proTeins ThaT may be made Binding a signal molecule as a hormone To a recepTor which Traverses cell membrane inTo a cell MAY CAUSE conformaTional changes aT The opposiTe end of The recepTor which in Turn may Trigger a cascade of molecular resTrucTuring inside a cell including reorienTaTion of The cyToskeleTon Mallery Molecules of Cells 17 SELFASSEMBLY of molecules inTo organelles andor cells inTo Tissue is noT much differenT from selfassembly of aToms inTo compounds The shape a molecules assumes is characTerisTic of The way The sTrucTure as a whole will behave in 3D space and maybe cells respond in a similar way according To rules of TensengTy Fully TriangulaTed TensegriTy sTrucTures once self assembled ma have been selecTed for Through evoluTion because of Their sTrucTural efficiency Their high mechanical sTrengTh amp minimal use of maTerials TensegriTy may be The mosT economical and efficienT way To build cell sTrucTure Mallery Molecules of Cells 18 SUMMARY a few fundamental principles ofchemistry are essential for understanding cellular processes at the molecular level 1 covalent and noncovalente lectrostatic forces control molecular shape amp form forces ofcon guration and conformation result in biologically active molecules gure 2 a 2 small molecules are the building blocks of larger molecules monomer make polymers make supramolecular complexes make organelles g 21 b 3 and 4 are to be covered under metabolism 3 chemical reaction are reversible depending on rate constants and the P amp R 21 4 source ofcellular chemical energy is he hydrolysis ofATP when high energy 5 phosphoanhydride bonds are broken by addition ofwater hydrolysi g 21 d Mallery Molecules of Cells 19 Bil 255 CMB Chemical Makeup of Living Cells Mallery Molecules of Cells Molecules of Living SysTems chapTer 2 pg 2950 The chemical properTies of The living sTaTe The sTrucTure of biological molecules how Their shape deTermines The roles They play in The complex chemical processes of life Even The mosT complicaTed biological molecules can be divided inTo smaller and smaller funcTional groups REDUCTIONISM Some Web Resources that give 3D shapes of Biomolecules A Site of the Molecules of Life mwk Mallery Molecules of Cells The chemicals of life ELEMENTS substances composed of atoms all having an identical number of protons can39T be reduced To simpler39 substances by normal chemical means only 30 of 92 elements OCCUR IN LIVING SYSTEMS 99 of LIVING MATTER is made of C H O N P 5 all have low atomic number39s amp are easily reactive amp form covalent bond Molecular composition of cells Water H20 70 Inorganic ions Na K CI P04 1 Small molecules aa s sugar nucleotides 5 Macromolecules protein na etc 24 Mallery Molecules of Cells Biomolecules Weak For39ces amp Design of Metabolism 1 BIOMOLECULES car39bon skeletons mostly carbon compounds are found in living systems WHY Car39bon 9 easily forms 4 covalent bonds thus makes many small biomolecules allows 3D shapes that can evoke biological activity possesses gr39eat chemical reactivity interacts with common chemical functional qroups Functional Groups groups of atoms acts as a unit give organic molecules their physical properties chemical reactivity amp solubility in aqueous solutions common functional qroups In biomolecular chemistry the concept of functional groups is useful as a basis for classification of large numbers of compounds according to their chemical properties and reactivity most groups possess electronegative atoms 0 N P S key bonds are ester COC amp amide CN most are ionizable at physiological pH 68 to 74 read pages 40 50 Mallery Molecules of Cells 4 2 small Biomolecules monomers Four majors groups of small biomolecules a SUGARS compounds with formula CH 20 n aldoses vs ke ioses rings g amp B links m isomers glucose vs galac iose glucose glucose mono disacc Tri golx saccharides n amp long chain polymers of monosaccharides b FATTY ACIDS long chain hydrocarbon sa iura ied vs unsa iura iedquot liEids Triacylglycerols animal fa is and ghospholipids of membranes easily self assembly in io aggrega ies san micelles n amp bilayers s39ieroid amp choles ierols 4 ring skele ion are lipids because i ey39re insoluble Mallery Molecules of Cells 5 C AMINO ACID5 Fig 221 EepTide bond hundreds known buT only 20 common in proTeins of cell once established in The IIprimordial cellquot cerTain small biomolecules as covalenT Themes E seem To have been preserved ThroughouT evoluTion ie They were favored energeTically d NUCLEOTIDES parTs niTrogen conTaining quotringquot compounds a niTrogenousbase linked To a 5carbon sugar ribose Si deoxyribose Sl a phosphaTe pyrimidines C T U purines A G nucleoTides form The energy rich compounds of cells as ATP Sl GTP as well as The nucleic acids Mallery Molecules of Cells Structural Chemistry orientation of covalent bonds in space molecular configuration results in specific bond angles and molecular geometry methane CH4 10950 atetrahedron formaldehyde HZCO with free rotation 120o same plane with no free rotation one key to shape is the ASSYM ETRIC CARBON a carbon atom bound to 4 dissimilar atoms in a nonplanar configuration tetrathedron results in 2 different spatial orientations producing CHIRAL molecules ones that are mirror images of each other optical or stereoisomers Mallery Molecules of Cells ENANTIOMERS molecules that are nonsuperimposable mirror images of one another called Stereoisomers two molecules are not equivalent or identical and have 2 molecular orientations or mirror images an optically active CHIRAL is not superimposable on its mirror image chiral animation stereoisomers may have mostly identical chemical properties but often rotate plane of polarized light via different angles LEVOROTARY L rotate light left negative optical rotation DEXTRORTATORY D rotate light right positive optical rotation and likely have different BIOLOGICAL ACTIVITY Parkinson39s Disease amp dihydroxyphenylalanine LDOPA figure Mallery Molecules of Cells Biological Activity amp the Shapes of Biomolecules Biological activity is catalytic ability of molecules to do work There are 2 properties of biomolecules which gives them their unique FITNESS for Biological Activity amp the Living State A CONFIGURATION the spatial arrangement of atoms in molecules configuration can39t be interconverted wo breaking bonds based upon COVALENT BOND sharing of outer orbital e39s between two atoms thereby forming a molecule examples of Covalent Configurations isomers based upon covalent bond configurations glu v gal Mallery Molecules of Cells 9 BIOLOGICAL ACTIVITY amp The Shape of Biomolecules B CONFORMATION or shape surface ouTline or conTour or 3D orienTaTion of chemical groups ThaT are free To assume differenT posiTions in space wiThouT breaking any bonds do primarily To FREE ROTATION of aToms abouT a single chemical bond WEAK NONCOVALENT FORCES hold aToms in spaTial arrays consequences of conformaTions differenT isomeric shapes forms of molecules can exisT only one of which may be biologically acTive oThers aren39T ENZYMES can disTinguish beTween biologically acTive forms isomers based upon The quotSHAPEquot of Thai isomer Mallery Molecules of Cells 10 Weak Molecular Forces of Life see Panel 27 99 78 Noncovaent Electrostatic Interactionsquot in the 10150 calmol IONIC bondsquot charged small ions atoms which gainedlost e39s which attract wo water they are very strong cgstals of NaCl DIPOLE attractions via asymmetrical internal distribution of charges in a molecule which has no net charge opposite poles attract DISPERSIONquot van der Waal39s Forces electrostatic attraction based upon closeness of atoms is important in macromolecular interactions for 3D shapes HYDROPHOBIC Interactions repulsion of electrostatic dipoles of water by non polars quotfattyhydrocarbonquot groups self assembly HYDROPHILIC Interactions substances that dissolve readily in water ions amp polar molecules water as a dipole surrounds amp solubilizes a solute molecule HYDROGEN bonds g electrostatic attraction between H of one atom and a pair of nonbonded e s on an acceptor group OH amp NH with O amp N Mallery Molecules of Cells 11 Covalent Molecular Forces of Life see table 21 pg 46 TYPE of BOND ENERGY Kclmol TYPE of INTERACTIONS ENERGY Kclmol SINGLE COVALENT BONDS OH 110 HH 104 CH 99 CO 84 CC 83 SH 81 CN 70 CS 62 DOUBLE BONDS CO 170 CN 147 CC 146 Mallery NONCOVALENT BONDS IONIC BONDS 10 50 HYDROGEN BONDS 10 20 VANDER WAALS 01 10 HYDROPHOBIC 01 10 Molecules of Cells 12 Biological Design or How Weak Molecular Forces amp Shape Build Form Is there fundamental principle guides biological organization in practice some commonuniversal rules of molecular assembly must exist one sees recurring patterns of spirals triangulated forms amp pentagons in everything from crystals to proteins viruses to plankton paramecia to protozoa Tensegrigy is an architectural principle of biological shape amp form How individual groups of molecules assemble themselves within whole living organisms is a fundamental question of the living condition Mallery Molecules of Cells 13 PRINCIPLE of SELFASSEMBLY molecules join To form larger amp more sTable sTrucTures ofTen wiTh new amp nonpredicTed properTies or emergenT properTies macromolecules gt organelles gt cells gt Tissues gt organs The answer may lie in The principles of TensegriTy The applicaTion of general archiTecTural principles To biomolecules amp living sysTems TENSEGRITY defines The mechanical rules and how sTrucTures are sTabilizedby balancing forces of inTernal Tension and compression Mallery Molecules of Cells 14
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