Chapter 1 Introduction to Biochemistry-1.ppt

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1. CHAPTER ONE
INTRODUCTION TO BIOCHEMISTRY
•DEFINITION
The term Biochemistry (bios= life) was first introduced by a
German chemist Carl Neuberg in 1903.
Biochemistry may be defined as a science concerned with the
chemical nature and chemical behaviour of the living matter.
It takes into account the studies related to the nature of the
chemical constituents of living matter, their transformations in
biological systems and the energy changes associated with these
transformations.
Such studies have been conducted in both the plant and animal
tissues.
Broadly speaking, biochemistry may thus be treated as a discipline
in which biological phenomena are analysed in terms of chemistry.
The branch of biochemistry, for the same reason, has been
variously named as Biological Chemistry or Chemical Biology.

2. Modernbiochemistryhastwobranches,descriptive
biochemistryanddynamicbiochemistry.
Descriptivebiochemistryisconcernedwiththe
qualitativeandquantitativecharacterizationofthevarious
cellcomponents.
Dynamicbiochemistrydealswiththeelucidationofthe
natureandthemechanismofthereactionsinvolvingthese
cellcomponents.
Itemergedasadistinctdisciplinearoundthebeginningof
the20thcenturywhenscientistscombinedchemistry,
physiologyandbiologytoinvestigatethechemistryofliving
systemsby:
A.Studyingthestructureandbehaviorofthecomplex
moleculesfoundinbiologicalmaterialand
B.thewaysthesemoleculesinteracttoformcells,tissues
andwholeorganism

3. Has a Wide Range of Applications
Biochemistryisappliedtomedicine,dentistry,andveterinary
medicine.
Infoodscience,biochemistsresearchwaystodevelopabundantand
inexpensivesourcesofnutritiousfoods,determinethechemical
compositionoffoods,developmethodstoextractnutrientsfromwaste
products,orinventwaystoprolongtheshelflifefoodproducts.
Inagriculture,biochemistsstudytheinteractionofherbicideswith
plants.Theyexaminethestructure-activityrelationshipsofcompounds,
determinetheirabilitytoinhibitgrowth,andevaluatethetoxicological
effectsonsurroundinglife
Biochemistryspillsoverintopharmacology,physiology,microbiology,
andclinicalchemistry.
Intheseareas,abiochemistmayinvestigatethemechanismofadrug
action;engageinviralresearch;conductresearchpertainingtoorgan
function;orusechemicalconcepts,procedures,andtechniquestostudy
thediagnosisandtherapyofdiseaseandtheassessmentofhealth.

4. 1.2 Chemical and biochemical reactions
What Are Chemical Reactions?
Achemicalreactionisaprocessthatchangessomechemical
substancesintoothers.
Asubstancethatstartsachemicalreactioniscalledareactant,and
asubstancethatformsasaresultofachemicalreactioniscalled
aproduct.
Duringachemicalreaction,thereactantsareuseduptocreatethe
products.
ChemicalReactionsandEnergy
Chemicalreactionsalwaysinvolveenergy.Whenmethaneburns,for
example,itreleasesenergyintheformofheatandlight.Other
chemicalreactionsabsorbenergyratherthanreleaseit.
EXOTHERMICREACTIONS
Achemicalreactionthatreleasesenergy(asheat)iscalled
anexothermicreaction.Thistypeofreactioncanberepresented
byageneralchemicalequation:
Reactants→Products+Heat

5. ENDOTHERMIC REACTIONS
Achemicalreactionthatabsorbsenergyiscalledanendothermic
reaction.Thistypeofreactioncanalsoberepresentedbyageneral
chemicalequation:
Reactants+Heat→Product
ACTIVATIONENERGY
Allchemicalreactionsneedenergytogetstarted.Evenreactionsthat
releaseenergyneedaboostofenergyinordertobegin.
Theenergyneededtostartachemicalreactioniscalledactivation
energy.Activationenergyislikethepushachildneedstostartgoing
downaplaygroundslide.
Thepushgivesthechildenoughenergytostartmoving,butonceshe
starts,shekeepsmovingwithoutbeingpushedagain.Activationenergyis
illustratedinFigurebelow

6. Biochemical Reactions and Enzymes
Biochemicalreactionsarechemicalreactionsthattakeplaceinsidethe
cellsoflivingthings.
Thefieldofbiochemistrydemonstratesthatknowledgeofchemistryas
wellasbiologyisneededtounderstandfullythelifeprocessesof
organismsatthelevelofthecell.
Thesumofallthebiochemicalreactionsinanorganismis
calledmetabolism.
Itincludesbothexothermicandendothermicreactions.

7. Exothermicreactionsinorganismsarecalledcatabolicreactions.
Thesereactionsbreakdownmoleculesintosmallerunitsandrelease
energy.
Anexampleofacatabolicreactionisthebreakdownofglucose,which
releasesenergythatcellsneedtocarryoutlifeprocesses.
Endothermicreactionsinorganismsarecalledanabolicreactions.
Thesereactionsbuildupbiggermoleculesfromsmallerones.
Anexampleofananabolicreactionisthejoiningofaminoacidstoform
aprotein.
Whichtypeofreactionscatabolicoranabolic?doyouthinkoccur
whenyourbodydigestsfood?
TYPES OF BIOCHEMICAL REACTIONS

8. 1.3.Chemistry of organelles (hierarchical organization of organelles
in living cells, composition, properties, and function of organelles)
MolecularOrganizationofacell

9. Hierarchy in the Molecular Organization of Cells
Precursorsfromtheenvironment(CO2,H2Oammonia,nitrogen)
Metabolicintermediates–(puruvate,citrate,malate,
glyceraldehyde-3-phosphate)
Buildingblocks(nucleotides,aminoacids,monosaccharides,
fattyacids)
Macromolecules(nucleicacids,proteins,polysaccharides,
lipids)
Supramolecularassemblies(ribosomes,enzyme
complexes,contractilesystems,microtubules)
Organelles(nucleus,mitochondria,golgicomplex,
endoplasmicreticulum,lysosomes)

10. The Cell
Aftersupramolecularassemblies,thenexthigherlevelof
organizationisthefundamentalunitoflife,thecell.
Scientistshavelongrecognizedtwobasicclassificationsof
organisms:
(1)theeukaryotes,organisms,includingplantsandanimals,whose
cellshaveadistinctmembrane-enclosednucleusandwell-defined
internalcompartmentation,and
(2)theprokaryotes,simple,unicellularorganisms,mainlybacteria
andblue-greenalgae,withneitheradistinctcellnucleusnoran
internalcellularcompartmentation.
Thisclassificationwasachievedprimarilybymicroscopicobservation
and,hence,isbasedonmorphologicalcellstructureandanatomy.
However,ifcellsareclassifiedbygeneticanalysis(DNAandRNA
sequences),thenthreedistincttypesarerecognized.
In1977,CarlWoese,nowattheUniversityofColorado,
discoveredthroughgeneticanalysisofribosomalRNAthat
archaebacteriaorarchaea(ancientbacteria)

11. Theprokaryoticorganisms,althoughtheleastdeveloped,arethemost
abundantandwidespreadoforganisms.
Severalcharacteristicsofprokaryoticcellscanbegeneralized:
1.Thesizemayrangefrom1to10μmindiameter.
Bacteria,anabundantprokaryoticorganism,havethreebasicshapes:
spheroidal(cocci),rodlike(bacilli),andhelicallycoiled(spirilla).
2.Thecellularcomponentsareencapsulatedwithinacellmembrane
andrigidcellwall.Occasionallythemembranemayinfoldtoform
multilayeredstructurescalledmesosomes.Theoutsidesurfaceisoften
coveredbyflagella,whichareappendagesforlocomotion,andpili,which
arestructuralfeaturesresponsibleforthetransferofDNAduringsexual
conjugationandforattachmenttosurfaces.
3.Theinteriorofthecell,calledthecytoplasm,isagel-like,
heterogeneoussuspensionofbiomoleculesincludingsmallmolecules,
solubleenzymes,ribosomes(supramolecularparticlesofRNAand
protein),andcoiledDNAinthenucleoidregion.
ProkaryoticCells

12. Figure1.1Schematicdiagramofatypicalprokaryoticcell.
4.Eachcellhasonechromosome,asinglecopyofDNA(thegenome).
Severalcopiesmaybepresentinarapidlygrowingcellthatreplicates
bysimpledivision.Theprokaryoticorganismthathasbeentheobjectof
mostbiochemicalstudiesistheEscherichiacoli(E.coli)bacterium.
Indeed,weknowmorebiochemistryaboutthisorganismthatlivesin
ourgutthananyother,includinghumans.Becausesomuchis
understoodaboutthisbacterium,ithasrecentlybeenpossibleto
preparepicturesoftheinteriorofalivingcell.

14. Eukaryotic Cells
Theclassofeukaryotesincludesplants,animals,fungi,protozoans,
yeasts,andsomealgae.
Thecellsfoundintheseorganismshavelittleincommonwiththe
prokaryotes.
Thecomplexeukaryoticcellsaremuchlarger,withdiametersranging
from10to100μm.
Theyaresurroundedbyaplasmamembranemadeupofproteinand
lipid
Thisisachemicalbarrierthroughwhichallmoleculesthatenteror
exitthecellmustpass.
Auniquefeatureoftheeukaryoticcellisthecompartmentationof
cellularcomponentsand,therefore,thecompartmentationof
biologicalfunction.

15. Figure Typical eukaryotic cells Animal Cell

16. Humanbodycontainsdifferentorganssuchastheheart,lungand
kidneyseachoneofwhichperformsdifferentfuntions.
ECalsohaveasetofintracellularcomponentscalledsubcellular
organellessomeofitsurroundedbyaprotectivemembrane.
Compositionandfunctionsoforganellesaredescribedbelow:
Plasmamembrane
Theouterliningofaeukaryoticcelliscalledplasmamembrane.
thisservestoseparateandprotectcellfromitssurrounding
environment.
itismadeupofadoublelayerofproteinsandlipids.
Cytoskeleton
Cytoskeletonisacomplexanddynamiccomponentthatactsto
organiseandmaintaincellshape,anchororganellsintheirplace,helps
duringendocytosis(uptakeofmaterialbythecell)andmoves
intracellularorganellesofthecellduringtheprocessesofgrowthand
motility.
Thereareanumberofproteinsassociatedwithcytoskeleton.
Composition and functions

17. Cytoplasm
Insidethecellthereisalargefluid–filledspacecalledcytoplasm.
Itislikesoupwithinwhichallthecellorganelles.
cytoplasmisalsoahomeforcytoskeleton.
Itcontainsseveralsaltsandisanexcellentconductorofelectricity,creating
environmentforthemechanicsofthecell.
Nucleus
Nucleus,alsocalledcellsinformationcentre,isthemostconspicuous
organellefoundinaeukaryoticcell.
IthousescellschromosomesandisaplacewherealmostalltheDNA
replicationandRNAsynthesisoccur.
Nucleusisspheroidalinshapeandisseparatedfromcytoplasmbya
membranecallednuclearenvelope.
Eukaryoticgeneticmaterialismorecomplexandisdividedintodiscrete
unitscalledgenes.
humangeneticmaterialismadeupoftwodistinctcomponentscallednuclrar
genomeandmitochondrialgenome.

18. Ribosome
Ribosomeisalargecomplexcomposedofmanymolecules,
includingRNAandproteins.
Theseareresponsiblefortheprocessingofgeneticinstruction
carriedbymRNA.
theprocessofconvertingmRNAcodonintothesequenceof
aminoacidsthatmakeupaproteiniscalledtranslation.
someoftheribosomefloatfreeinthecytoplasm,calledfree
ribosomewhileothersareboundtoendoplasmicreticulum.
Mitochondriaandchloroplasts
Thesearepowergeneratorandself-replicatingorganelles.
theyoccurinvariousnumbers,shapesandsizesinthe
cytoplasmofalleukaryoticcells.
Boththeorganellesaresurroundedbyadoublemembrane
withanintermembranespace.
theyhavemanyfolding,fillingtheirinnerspace.theyhavetwo
functionallydistinctmembranesystems,inwardfolds
arecalledcristae.

19. Chloroplastaresimilartomitochondriabutarefoundinplants
wheretheyconvertlightenergy(fromthesun)intoATPthrough
theprocesscalledphotosynthesis.
Endoplasmic recticulam and golgi apparatus
ERisthetransportnetworkformolecules.Itispresentintwo
formscalledroughendoplasmicreticulum(RER)andsmooth
endoplasmicreticulum(SER).
Proteinsthataretobeexportedoutofthecellarepassestothe
Golgiapparatus,alsocalledgolgibodiesorGolgicomplex.
Lysosomes and peroxisomes
Theyarealsoreferredasgarbagedisposalsystemofthe
cell.botharespherical,boundbyasinglemembrane
andarerichindigestiveenzymesfordegrading
proteins,nucleicacidsandpolysaccharidesthatwork
aslowpH.animportantfunctionoflysosomeisto
digestforeignbacteriathatinvadethecell.

20. Theyalsohelpinrecyclingofreceptorproteinsandother
membranecomponents,helpinrepairofthedamagetoplasma
membrane.
Peroxisomesfunctiontogetthebodyoftoxicsubstancessuchas
hydrogenperoxideorothermetabolites,andcontainenzymefor
enzymeutilization.
highernumberofperoxisomescanbefoundinliverwheretoxic
by-productsareknowntoaccumulate.
Itresemblelysosomes.
peroxisomesareself-replicatingwhereaslysosomesareformedin
Golgicomplex.
Centrosome
Centrosomecalledcytoskeletonorganizer,produce
microtubulesofacell,whichisthekeycomponentof
cytoskeleton.
cetrosomesarecomposedoftwocentrioles.asinglecentrosome
ispresentinanimalcells.itfoundinsomefungi
andalgae.

22. Vacuoles
Vacuolesstorefoodandwasteproducts.Somevacuolesalsostore
waterandaredescribedasliquid–filledspaces.theyare
surroundedbyamembrane.
Cell membrane
Itreferstotheoutercoveringofthecellandisfoundinallliving
cells.itisahighlyviscous
structure.
Fluid-mosaicmodelofcellmembrane
Biologicalmembraneshavesuchastructurewheresomeproteins
spanalipidbilayerwhileothersarepartiallyimmersed.thisiscalled
Fluid-mosaicmodelasamembraneconsistsofmosaicofproteinsand
lipids.

24. FUNCTION OF CELL MEMBRANE
1.cellmembranemaybeassociatedwithseveralenzymese.g.
Phospholipaseareusedasmarkersofcellmembrane.
2.Membranesalsocontainspecificreceptorsforexternalstimuli
suchashormones.afterahormonebindstoitsreceptor,itgenerates
signalsandregulatesintracellularactivities.
3.carbohydratescomponentsofglycoproteinsinamembraneactas
recognitionsitesforseveralsubstancesuchasantibodies.
4.Amembranealsoactsasabarriertherebylossofuseful
substanceswhilepermittingentryofnutrients,
thusitisimportantintransportofsubstances.

26. Chapter 2 Water PH and Buffer
1. How is the molecular structure
of water related to physical and
chemical behavior?
2. What is a Hydrogen Bond?
3. What are Acids and Bases?
4. What is pH, and what does it
have to do with the properties of
Water?
5. What are Titration Curves?
6. What are buffers, and why they
are important?

28. Non-covalent Bonding
1) Electrostatic interactions
by coulombs law F= kq
1q
2 / r
2
Dq are chargesr is radius
D = dielectric of the media, a shielding of charge.
And k =8.99 x10
9
Jm/C
2
D = 1 in a vacuum
D = 2-3 in grease
D = 80 in water
Responsible for ionic bonds, salt linkages or ion pairs,
optimal electrostatic attraction is 2.8Å

29. Dielectric effect D
hexane 1.9
benzene 2.3
diethyl ether 4.3
CHCl
3 5.1
acetone 21.4
Ethanol 24
methanol 33
H
2O 80
HCN 116
H
2Oisanexcellentsolventanddissolvesalargearray
ofpolarmolecules.
However,italsoweakensionicandhydrogenbonds
Therefore,biologicalsystemssometimesexcludeH
2O
toformmaximalstrengthbonds!!

30. 2)Hydrogen bonds
O-H N N-H O
2.88 Å 3.04 Å
H bond donor or an H bond acceptor
NH OC
3-7 kcal/mol or 12-28 kJ/mol
very strong angle dependence

31. 3)van der Waals attraction
Non-specific attractions 3-4 Å in distance (dipole-dipole attractions)
Contact Distance
Å
H 1.2 1.0 kcal/mol
C 2.0 4.1 kJ/mol
N 1.5 weak interactions
O 1.4 important when many atoms
S 1.85 come in contact
P 1.9
Can only happen if shapes of molecules match

33. Structure & Properties of Water
Bent geometry, O-H bond length of 0.958Å
Can form Hydrogen bonds

34. Hydrogen Bonds
Physical properties of ice and water are a result of
intermolecular hydrogen bonding
Heat of sublimation at 0
o
C is 46 kJ/mol yet only 6 kJ/mol is
gaseous kinetic energy and the heat of fusion of ice is 6
kJ/mol which is only 15% of the energy needed to melt ice.
Liquid water is only 15% less hydrogen bonded than ice
CH
4boils at -164
o
C but water is much higher.

35. A hydrogen bond between two
water molecules

36. The structure of ice

37. The structure of water is irregular
•Heat of sublimation of ice is
46.9 kJ/mol
•41 kJ/mol from hydrogen
bonds.
•Only 15% of the hydrogen
bonds are disrupted by melting
•Short term interactions are
tetrahydral in nature
•Water reorients once in 10
-12
sec that is a pico second

38. Water of Hydration
•Hydration -to be surrounded by H
2O
•A polar molecule is hydrated by the partial charge
interaction of the water molecule
•Multiple H bonds increase solubility
Solvation of ions

39. Forms Hydrogen bonds with Functional Groups

40. Free energy of transfer for hydrocarbons from
water to organic solvent
The Hydrophobic effect

41. Nonpolar/Polar Interactions and Structured Water
A cage of water molecules (calatherate)
surrounding the non-polar molecule.
This cage has more structure than the
surrounding bulk media.
DG = DH -TDS
To minimize the structure of
water the hydrophobic
molecules cluster together
minimizing the surface area.

42. Amphiphiles
•Most biological molecules contain bothpolarand
non-polar segments
•They are at the same timehydrophobicand
hydrophilic

43. Amphiphiles: both polar and non-polar
Detergents, Fatty acids, lipid molecules
•polar head; non-polar tail.
•Water is more concentrated than the molecules it
surrounds so the shear numbers of ordered
molecules is much greater. The greatest entropy
is a function of both the dissolved molecule and
the solvent.
•Proteins are also amphipathic and hydrophobic
interactions are the greatest contributor the three
dimensional shape of proteins.

44. Amphiphiles form micelles, membrane
bilayes and vesicles
•A single amphiphile is surrounded by water,
which forms structured “cage” water. To minimize
the highly ordered state of water the amphiphile is
forced into a structure to maximize entropy
DG = DH -TDS driven by TDS

45. Osmosis
Diffusion

46. Key Concepts:
Noncovalent bonds play important roles in determining
the physical and chemical properties of water. They also
have a significant effects on the structure and function of
biomolecules.
H-bonding is responsible for water’s high freezing and
boiling points. Because water has a high heat capacity, it
can absorb and release heat slowly. Water plays an
important role in regulating heat in living organisms.

47. 4)Hydrophobic interactions
Non-polar groups cluster together
DG = DH -TDS
The most important parameter for determining a biomolecule’s shape.
Entropy order-disorder. Nature prefers to maximize entropy
“maximum disorder”.