Basics of Organic Chemistry, Biochemistry

Basic Organic Chemistry

1. Basics of
Organic Chemistry
MC 2| Biochemistry

2. ORGANIC CHEMISTRY & BIOCHEMISTRY
•Themoleculesthatbridgechemistryand
biology.
•Mostcommonelements:C,H,O,N
•OrganicChemistry:studyofcompounds
containingcarbon
•Biochemistry:thestudyofchemistryof
livingsystems
Basics of Organic Chemistry
MC 2| Biochemistry

3. Historical Development of Organic Chemistry
•Historically,thetermorganicchemistrydatesthelate
1700s,whenitwasusedtomeanthechemistryof
compoundsfoundinlivingorganisms.
•Earlychemiststhoughtorganiccompounds couldbe
producedonlythroughtheactionofa“vitalforce,”a
specialforceactiveonlyinlivingorganisms
Butorganiccompoundsdonotnecessarilybederivedfromliving
organisms.
Basics of Organic Chemistry
MC 2| Biochemistry

4. Historical Development of Organic Chemistry
FriedrichWöhler,1828
Basics of Organic Chemistry
MC 2| Biochemistry

5. Historical Development of Organic Chemistry
Basics of Organic Chemistry
MC 2| Biochemistry
Friedrich Wöhlerdiscovered in 1828 that it was possible to convert the “inorganic” salt
ammonium cyanateinto the “organic” substance urea, which had previously been found in
human urine.
Started in 1828-Wohler (German chemist) showed that urea, an organic
compound naturally formed in the liver from amino acids could be produced in
the laboratory by heating ammonium cyanate, an inorganic compound.
➢Previous belief: organic compounds could only be made by living cells or organs
of plants and animals that is only lifeless or inorganic compounds could be made
in the lab.
➢Organic compounds were originally named such –they were thought to be present
in living organisms or materials that were derived from them, hence the term
organic.

6. Why is Carbon special?
•Asagroup4Aelement,carboncan
sharefourvalenceelectronsandform
fourstrongcovalentbonds.
•Furthermore,carbonatomscanbond
toitselforwithotherelements.
•Carbon is tetravalent.
-August Kekuléand Archibald Scott Couper, 1858
Basics of Organic Chemistry
MC 2| Biochemistry

7. FUNCTIONAL GROUP
Auniquereactivecombinationofatomsthatdifferentiates
moleculesoforganiccompoundsofoneclassfromthose
ofanother.
Basics of Organic Chemistry
MC 2| Biochemistry

8. FUNCTIONAL GROUP
Basics of Organic Chemistry
MC 2| Biochemistry

9. FUNCTIONAL GROUP
Basics of Organic Chemistry
MC 2| Biochemistry

10. FUNCTIONAL GROUP
Basics of Organic Chemistry
MC 2| Biochemistry

11. Methods of Writing Formulas
Basics of Organic Chemistry
MC 2| Biochemistry
Expandedstructuralformula-Astructuralmolecularformulashowingallthe
covalentbonds.
Condensedstructuralformula-Astructuralmolecularformulashowingthe
generalarrangementofatomsbutwithoutshowingallthecovalentbonds.

12. Sample Problem
Basics of Organic Chemistry
MC 2| Biochemistry
Writeacondensedstructuralformulafor
eachofthefollowingcompounds

13. HYDROCARBONS
Basics of Organic Chemistry
MC 2| Biochemistry
Hydrocarbons,thesimplestofallorganiccompounds,containonly
carbonandhydrogen.
Saturatedhydrocarbonsoralkanesareorganiccompoundsin
whichcarbonisbondedtofourotheratomsbysinglebonds;there
arenodoubleortriplebondsinthemolecule.
Unsaturatedhydrocarbonsarecalledalkenes,alkynes,and
aromaticsandcontaindoublebonds,triplebonds,orsix-carbon
rings

14. Basics of Organic Chemistry
MC 2| Biochemistry

15. Basics of Organic Chemistry
MC 2| Biochemistry

16. ALKANES
Basics of Organic Chemistry
MC 2| Biochemistry
•Saturatedhydrocarbons
•SinglebondsbetweenC-C&C-H
•Nootheratoms(hydrocarbon)
•Canbeopenchainorcyclic

17. STRUCTURAL ISOMERS
Basics of Organic Chemistry
MC 2| Biochemistry
•Compounds withthesamemolecularformulabutdifferent
connectionsofatomsarecalledstructuralisomers.
•Structuralisomershavedifferentphysicalandchemical
properties
Forexample,C₅H₁₂:

18. Sample Problem
Basics of Organic Chemistry
MC 2| Biochemistry

19. NOMENCLATURE (IUPAC)
Basics of Organic Chemistry
MC 2| Biochemistry
Bynumberofcarbonatoms(Prefixes)
•1carbon=meth
•2carbons=eth
•3carbons=prop
•4carbons=but
[pent,hex,hep,oct,…]
Linear:n-
Cyclic:cyclo
Halogen:fluoro,chloro,bromo,…
Morethanonesubstituent:
(ofthesamekind)
•Two:di
•Three:tri
•Four:tetra
Forcompounds(Suffixes)
•Alkane=ane
•Alkene=ene
•Alkyne=yne
•Alcohols=ol

20. ALKANE NOMENCLATURE
Basics of Organic Chemistry
MC 2| Biochemistry

21. How to name a compound
Basics of Organic Chemistry
MC 2| Biochemistry
Step1.Findthelongestcontinuouschain.
Step 2. Number the chain from the end nearest the
first substituent encountered.
Step3.Nameeachsubstituent.
Step4.Beginthenamewiththenumber(s)onthe
Catom(s)towhicheachsubstituentisbonded.
Step5.Whentwoormoresubstituentsarepresent,
listthemalphabetically(ignoringtheprefixwhen
alphabetizing)

22. Examples
Basics of Organic Chemistry
MC 2| Biochemistry

23. Examples
Basics of Organic Chemistry
MC 2| Biochemistry
Drawacondensedstructuralformulaandbond-linestructurefor
3-ethyl-2-methylhexane.

24. Iso, sec-, and tert-
Basics of Organic Chemistry
MC 2| Biochemistry
The only prefix which is used when putting the substituents in alphabetical order isiso as in
isopropyl or isobutyl.The prefixes sec-and tert-are not used

25. Iso, sec-, and tert-
Basics of Organic Chemistry
MC 2| Biochemistry

26. ALKENES
Basics of Organic Chemistry
MC 2| Biochemistry
•Unsaturatedhydrocarbons
•Haveatleastonedoublebond
Nomenclature
1.Identifylongestcontinuouscarbonchainthatincludesthealkene.
2.Numbertogivethealkenethelowestpossiblenumber
3.Nameendsin–ene
4.Assigncis/transorE/Ztoanyalkenesthatcanexhibitcis/transisomerism

27. Examples
Basics of Organic Chemistry
MC 2| Biochemistry

28. ALKYNES
Basics of Organic Chemistry
MC 2| Biochemistry
•Unsaturatedhydrocarbons
•Haveatleastonetriplebond
Nomenclature
1.Identifylongestcontinuouscarbonchainthatincludesthealkyne.
2.Numbertogivethealkynethelowestpossiblenumber
3.Nameendsin–yne

29. ALKYNES
Basics of Organic Chemistry
MC 2| Biochemistry

30. AROMATIC COMPOUNDS
Basics of Organic Chemistry
MC 2| Biochemistry
•Cyclicmoleculeswithalternatedunsaturatedbonds
leadtoapropertycalledaromaticity.

31. Nomenclature of Benzene Derivatives
Basics of Organic Chemistry
MC 2| Biochemistry
Guideline1.Whenasinglehydrogenofthebenzenering
isreplaced,thecompound canbenamedasa
derivativeofbenzene:

32. Nomenclature of Benzene Derivatives
Basics of Organic Chemistry
MC 2| Biochemistry
Guideline2.Anumberofbenzenederivativesareknown
bycommonnamesthatarealsoIUPAC-acceptedand
areusedpreferentiallyoverotherpossibilities.Thus,
tolueneisfavoredovermethylbenzene,andanilineis
usedratherthanaminobenzene:

33. Nomenclature of Benzene Derivatives
Basics of Organic Chemistry
MC 2| Biochemistry

34. Nomenclature of Benzene Derivatives
Basics of Organic Chemistry
MC 2| Biochemistry
Guideline3.Whentwogroupsareattachedtoa
benzenering,threeisomericstructuresarepossible.They
canbedesignatedbytheprefixesortho(o),meta(m),
andpara(p):

35. Nomenclature of Benzene Derivatives
Basics of Organic Chemistry
MC 2| Biochemistry
Guideline4.Whentwoormoregroupsareattachedtoa
benzenering,theirpositionscanbeindicatedby
numberingthecarbonatomsoftheringsoastoobtain
thelowestpossiblenumbersfortheattachmentpositions.

36. ALCOHOLS
Basics of Organic Chemistry
MC 2| Biochemistry
•Havean–OH group
Nomenclature
1.Identifylongestcontinuouscarbonchainthatincludesthealkyne.
2.NumbertogivetheOHthelowestpossiblenumber
3.Nameendsin–ol

37. ALCOHOLS
Basics of Organic Chemistry
MC 2| Biochemistry
NamethefollowingalcoholsaccordingtotheIUPACsystem:

38. CLASSIFICATION OF ALCOHOLS
Basics of Organic Chemistry
MC 2| Biochemistry
Primaryalcohol
AnalcoholinwhichtheOHgroupisattachedtoCH₃
ortoacarbonattachedtooneothercarbonatom.
Secondaryalcohol
AnalcoholinwhichthecarbonbearingtheOH
groupisattachedtotwoothercarbonatoms.
Tertiaryalcohol
AnalcoholinwhichthecarbonbearingtheOH
groupisattachedtothreeothercarbonatoms.

39. ALCOHOLS
Basics of Organic Chemistry
MC 2| Biochemistry
Classifythefollowingalcoholsasprimary,secondary,ortertiary:

40. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Apromisinganticancerdrug,taxol,isisolated
fromthebarkofthePacificyewtree.Though
taxolisacomplexcompound,whatdoesits
namesuggestaboutitsstructure?

41. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Alcoholsareveryimportantbiologicallybecausethealcoholfunctionalgroup
occursinavarietyofcompounds associatedwithbiologicalsystems.For
example,sugarscontainseveralhydroxygroups,andstarchandcellulose
containthousandsofhydroxygroups

42. PHENOLS
Basics of Organic Chemistry
MC 2| Biochemistry
Phenols are compounds in which an –OH group is connected to
a benzene ring.

43. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Indilutesolutions,phenolisusedasanantisepticanddisinfectant.The
derivativesofphenol,o-phenylphenoland2-benzyl-4-chlorophenol,are
ingredientsinLysol®,adisinfectantforwallsandfurnitureinhospitalsandhomes

44. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Otherimportantphenolsactasantioxidantsbyinterferingwithoxidizing
reactions.

45. ETHERS
Basics of Organic Chemistry
MC 2| Biochemistry
Ethers are formed by dehydration between alcohol molecules
and are used as solvents for organic reactions

46. ETHERS
Basics of Organic Chemistry
MC 2| Biochemistry
Nomenclature:
•Common namesforethersareobtainedbyfirstnamingthetwo
groupsattachedtotheoxygenandthenaddingthewordether.If
thegroupsarethesame,itisappropriatetousetheprefixdi-,asin
diethylether

47. ETHERS
Basics of Organic Chemistry
MC 2| Biochemistry
Nomenclature:
•IntheIUPACnamingsystemforethers,the–O–Rgroupiscalledan
alkoxygroup.The-ylendingofthesmallerRgroupisreplacedby-
oxy.

48. CYCLIC ETHERS
Basics of Organic Chemistry
MC 2| Biochemistry

49. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
AnestheticEthers:
Thewordetherisoftenassociatedwithgeneralanestheticsbecauseof
thewell-knownuseofethyletherforthispurpose.Ethyletherbecame
generallyusedasananestheticforsurgicaloperationsinabout1850.
However,theirusehassignificantlydiminishedduetosafetyconcerns
andthedevelopmentofmoreeffectiveandsaferanestheticagents.

50. THIOLS
Basics of Organic Chemistry
MC 2| Biochemistry
Sulfurandoxygenbelongtothesamegroupoftheperiodic
table,soitisnotsurprisingthattheyformsimilarcompounds.The
sulfurcounterparts(analogues)ofalcoholscontainan–SH
groupratherthanan–OHgroupandarecalledthiols(anolder
nameismercaptans).

51. THIOLS
Basics of Organic Chemistry
MC 2| Biochemistry
Nomenclature:
•Nameendswiththewordthiol

52. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Perhapsthemostdistinguishing
featureofthiolsistheirstrongand
disagreeableodors.
Skunksusethiolchemistryasan
effectivedefensemechanism.

53. CARBONYL GROUPS
Basics of Organic Chemistry
MC 2| Biochemistry
Thecarbonylfunctionalgroupischaracteristicofmanyorganic
compounds.Inacarbonylgroup,acarbonisdoublebondedtoan
oxygenatomandsinglebondedtotwootheratoms,forexample:
Aldehyde:CarbonylbondedtoatleastoneH
Ketone:Twocarbonatomsarebondedtothecarbonylgroup

54. CARBONYL GROUPS
Basics of Organic Chemistry
MC 2| Biochemistry

55. ALDEHYDE NOMENCLATURE
Basics of Organic Chemistry
MC 2| Biochemistry
•IntheIUPACsystem,aldehydesarenamedbyselectingthe
longestchainthatincludesthecarbonylcarbon.
•The-eofthealkanethathasthesamenumberofcarbonsis
replacedby-al.
•Becausethecarbonylcarboninaldehydesisalwaysattheend
ofthechain,itisalwaysdesignatedascarbonnumber1

56. KETONE NOMENCLATURE
Basics of Organic Chemistry
MC 2| Biochemistry
•InnamingketonesbytheIUPACsystem,thelongestchainthat
includesthecarbonylgroupisgiventhenameofthe
correspondingalkane,withthe-ereplacedby-one.
•Thechainisnumberedfromtheendclosesttothecarbonyl
group,andthecarbonylgrouppositionisindicatedbya
number

57. Basics of Organic Chemistry
MC 2| Biochemistry

58. KETONE NOMENCLATURE
Basics of Organic Chemistry
MC 2| Biochemistry
Name the following according to the IUPAC system

59. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Formaldehyde(HCHO):Formaldehydeisusedas
adisinfectantandpreservativeinmedical
laboratories.It'salsousedinsomemedical
proceduresfortissuepreservationandfixation.
However,duetoitstoxicnature,itsuseiscarefully
controlled.
Glutaraldehyde:Thisaldehydeisusedasa
disinfectantandsterilantformedicalequipment
andinstruments.It'sparticularlyeffectiveagainst
bacteria,viruses,andspores.

60. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Corticosteroids:Somecorticosteroidmedications
containketonefunctionalgroups.Thesemedications
areusedtotreatarangeofconditions,including
inflammation,allergicreactions,autoimmune
disorders,andmore.
KetoneBodies:Inthecontextofmetabolism,ketone
bodies(acetone,acetoacetate, and beta-
hydroxybutyrate)areproducedwhenthebody
breaksdownfattyacidsforenergyintheabsenceof
sufficientglucose.Elevatedketonelevelscanbe
indicativeofcertainmetabolicstates,suchas
diabeticketoacidosis.

61. CARBOXYLIC ACIDS
Basics of Organic Chemistry
MC 2| Biochemistry
Thecharacteristicfunctionalgroupofcarboxylicacidsisthe
carboxylgroup:

62. CARBOXYLIC ACIDS
Basics of Organic Chemistry
MC 2| Biochemistry
Nomenclature:
•Thelongestcarbonchainincludingthecarboxylgroupisfoundand
numbered.
•Thenumberingbeginswiththecarboxylcarbon,soinmonocarboxylic
acidsitisalwayslocatedatthebeginningofthechain,andno
numberisneededtolocateit.
•Thefinal-eoftheparenthydrocarbonisdropped,andtheending-
oicisadded,followedbythewordacid.
•Groupsattachedtothechainarenamedandlocatedasbefore.
•Aromaticacidsaregivennamesderivedfromtheparentcompound,
benzoicacid.

63. CARBOXYLIC ACIDS
Basics of Organic Chemistry
MC 2| Biochemistry
UseIUPACrulestonamethefollowingcarboxylicacids:

64. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Carboxylicacidswithlong
hydrocarbonchains,generally
12to20carbonatoms,are
calledfattyacids.

65. ESTERS
Basics of Organic Chemistry
MC 2| Biochemistry
Averyimportantreactionoccurswhencarboxylicacidsare
heatedwithalcoholsorphenolsinthepresenceofanacid
catalyst.Amoleculeofwatersplitsoutandacarboxylicesteris
formed

66. ESTERS
Basics of Organic Chemistry
MC 2| Biochemistry
Estersarewidelyfoundinfruitsandflowers,manyestersarevery
fragrantandrepresentsomeofnature’smostpleasantodors.
Becauseofthischaracteristic,estersarecommonlyusedas
flavoringagentsinfoodsandasscentsinpersonalproducts.

67. ESTERS
Basics of Organic Chemistry
MC 2| Biochemistry
Nomenclature:
Thenameofestersarebasedonthecarboxylicacidandalcohol
fromwhichtheyareproduced.

68. AMINES AND AMIDES
Basics of Organic Chemistry
MC 2| Biochemistry
Aminesareorganicderivativesofammonia,NH₃.

69. AMINES AND AMIDES
Basics of Organic Chemistry
MC 2| Biochemistry
Classify each of the following amines as primary, secondary, and
tertiary:

70. AMINES AND AMIDES
Basics of Organic Chemistry
MC 2| Biochemistry
Nomenclature:
Commonnamesareusedextensivelyforthosewithlowmolecular
weights.Thesearenamedbyalphabeticallylinkingthenamesof
thealkyloraromaticgroupsbondedtothenitrogenandattaching
thesuffix-amine.Thenameiswrittenasoneword,andtheprefixes
di-andtri-areusedwhenidenticalalkylgroupsarepresent

71. AMINES AND AMIDES
Basics of Organic Chemistry
MC 2| Biochemistry
Nomenclature:
•Therootnameisdeterminedbythelongestcontinuouschainof
carbonatoms.
•The-eendinginthealkanenameischangedto–amine.
•Thepositionoftheaminogrouponthechainisshownby
anumber.
•Numbersarealsousedtolocateothersubstituentsonthecarbon
chain.
•AnitaliccapitalNisusedasaprefixforasubstituentonnitrogen.

72. AMINES AND AMIDES
Basics of Organic Chemistry
MC 2| Biochemistry
Nomenclature:

73. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Amines as Neurotransmitters
•Neurotransmitterisachemical
messengerofthenervoussystem,
carrynerveimpulsesfromone
nervecell(neuron)toanother

74. Chemistry Around Us
Basics of Organic Chemistry
MC 2| Biochemistry
Amines as Neurotransmitters
Themostimportantneurotransmittersareacetylcholineandthree
otheramines:norepinephrine,dopamine,andserotonin:

75. ACTIVITY
Basics of Organic Chemistry
MC 2| Biochemistry
1. Draw the condensed structural formula for:
a.) 1-ethyl-1-propylcyclopentane
b.) 3-ethyl-2-pentanone
c.) 2-bromobutanal
2. Assign IUPAC names to the following compounds
3.) Determine the functional group present: