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Matter
Matter refers toanything that hasmass and takes up space.
All matter is composedof certain basicsubstances called
elements.
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There are 92 naturally
occurring elements,which serve as building
blocks of all matter.
C, H, O, N, P, SC, H, O, N, P, S the six elementsthe six elements
that are basic to life andthat are basic to life andcomprising about 95% of thecomprising about 95% of the
body weight of organisms.body weight of organisms.
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Types of Matter SolidSolid
--with definite shape andwith definite shape and
volumevolume
--molecules are compactlymolecules are compactly
arranged so that no spacesarranged so that no spacesexist between them.exist between them.
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Liquid-- no definite shape.no definite shape.
--assumes the shape of theassumes the shape of the
container where it is placed.container where it is placed.
-- molecules are loosely boundmolecules are loosely bound
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Gas-- tends to separate from onetends to separate from one
another and fills up anyanother and fills up anycontainer where it iscontainer where it isplaced.placed.
-- molecules are far apartmolecules are far apartfromfrom each other and are ineach other and are in
constant motion.constant motion.-- no definite volume.no definite volume.
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ATOMS ARE NATURES
BUILDING MA
TER
IA
LS AllAll substancessubstances areare composedcomposed
ofof tinytiny particlesparticles calledcalled
ATOMSATOMS..
ATOMATOM thethe smallestsmallest partpart ofof
anan element,element, whichwhich displaysdisplaysthethe propertiesproperties ofof thethe elementelement..
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Subatomic Particles____________________________________________________________________________________________
ParticleParticle ElectricElectric AtomicAtomic LocationLocation
ChargeCharge MassMass
____________________________________________________________________________________________
ProtonProton +1+1 11 NucleusNucleusNeutronNeutron 00 11 NucleusNucleus
ElectronElectron --11 00 ElectronElectron
shell/shell/orbitalorbital
____________________________________________________________________________________________
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ATOMIC NUMBERATOMIC NUMBER
--the number of protons inthe number of protons inan element.an element.
ATOMIC MASSATOMIC MASS
-- the sum of the protonsthe sum of the protonsand neutrons in an atom.and neutrons in an atom.
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ISOTOPESISOTOPES
-- atomsatoms ofof thethe samesame elementelementthatthat differdiffer inin theirtheir numbernumber ofofneutronsneutrons butbut havehave thethe samesamenumbernumber ofof protonsprotons..
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MOLECULES and COMPOUNDSMOLECULES and COMPOUNDS
Molecule formed whentwo or more atoms bond together.
Compound formed when
atoms of two or more differentbond together.
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TWO TYPES OF BONDS
IonicIonic BondBond aa chemicalchemicalbondbond formedformed byby thethe transfertransfer ofof
electron(s)electron(s) betweenbetween atomsatoms.. ThisThisalsoalso formedformed byby thethe attractionattraction ofofanionanion (negatively(negatively chargedcharged ion)ion)
andand cationcation (positively(positively chargedchargedion)ion)..
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Covalent BondCovalent Bond
-- aa chemicalchemical bondbondcharacterizedcharacterized byby thethe sharingsharing ofof
electronselectrons betweenbetween twotwo atomsatoms.. TypesTypes ofof CovalentCovalent BondsBonds::
aa.. NonpolarNonpolarC
ovalentC
ovalent BondBondbb.. PolarPolar CovalentCovalent BondBond
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CHEMISTRY OFCHEMISTRY OF
WATERWATER
Water Water aa polarpolar moleculemolecule
composedcomposed ofof 22 hydrogenhydrogen andand 11oxygenoxygen atomsatoms andand constitutesconstitutes 7070--9090%% ofof livingliving materialmaterial..
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Properties of Water:Properties of Water:
high heat capacity
high heat of vaporization
high polarity
molecules are cohesive and
adhesive
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high surface tensionhigh surface tension
high heat of fusion
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ACIDS and BASES
AcidsAcids-- anyany substancesubstance thatthat
dissociatesdissociates inin water,water, releasingreleasing
hydrogenhydrogen ionsions (H(H++
))..-- solutionsolution thatthat hashas aa highhighHH++ concentrationconcentration..
ExampleExample:: HydrochloricHydrochloric acidacidHClHCl HH++ ++ ClCl--
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Bases
-- anyany substancessubstances thatthat eithereithertakestakes upup hydrogenhydrogen ionsions (H(H++)) ororreleasesreleases hydroxidehydroxide ionsions (OH(OH--))..
--solutionsolution thatthat hashas highhigh OHOH--concentrationconcentration..
ExampleExample:: NaOHNaOH NaNa++ ++ OHOH--
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pHpH a measure to determine thea measure to determine the
acidity or alkalinity of solutions.acidity or alkalinity of solutions.
pH 0pH 0 6.9 (acidic)6.9 (acidic)
pH 7 (neutral)pH 7 (neutral)
pH 7.1pH 7.1 14 (alkaline)14 (alkaline)
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BUFFERBUFFER
-- aa chemicalchemical oror aa mixturemixture ofofchemicalschemicals thatthat keepkeep pHpH withinwithin
normalnormal limitslimits
-- resistsresists pHpH changeschanges bybytakingtaking upup excessexcess hydrogenhydrogen ionsions(H(H++)) oror hydroxidehydroxide ionsions (OH(OH--))..
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BUFFERFORMATIONBUFFERFORMATION
HH22O + COO + CO22 HH22COCO33HH++ + HCO+ HCO33
--
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Organic MoleculesOrganic Molecules
-- moleculesmolecules thatthat alwaysalwayscontaincontain carboncarbon (C)(C) andand hydrogenhydrogen(H)(H)..
-- thethe frameworkframework ofofbiologicalbiological moleculesmolecules consistsconsists ofofcarboncarbon bondedbonded toto otherothermoleculesmolecules oror otherother typestypes ofofatomsatoms..
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MonomerMonomer
-- (simple(simple organicorganic molecule)molecule)areare linkedlinked togethertogether withwith otherother
monomersmonomers toto form form aaPOLYMERPOLYMER..
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_________________________________
Polymer Monomer
_________________________________
CarbohydrateCarbohydrate MonosaccharideMonosaccharide
ProteinProtein AminoAmino AcidAcid
NucleicNucleic AcidAcid NucleotideNucleotide
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Functional GroupsFunctional Groups
-- specificspecific groupsgroups ofof atomsatomsattachedattached toto carboncarbon backbonesbackbones
ofof anan organicorganic moleculemolecule..--determines thedetermines the
characteristics, solubility andcharacteristics, solubility andchemistry of the molecule.chemistry of the molecule.
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Important Functional GroupsImportant Functional Groups
in Biological Moleculesin Biological Molecules
------------------------------------------------------------------------------------------------------------------GroupGroup ChemicalChemical PropertiesProperties FoundFound
FormulaFormula inin------------------------------------------------------------------------------------------------------------------
HydrogenHydrogen HH PolarPolar andand nonnon-- almostalmost allall
polar,polar, involvedinvolved organicorganic
inin condensationcondensation moleculesmolecules
andand hydrolysishydrolysis
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Continuation:Continuation:------------------------------------------------------------------------------------------HydroxylHydroxyl OHOH-- polar, involved inpolar, involved in Carbohydrates,Carbohydrates,
condensation andcondensation and nucleic acids,nucleic acids,
hydrolysishydrolysis alcoholsalcohols
CarbonylCarbonyl --C=OC=O polarpolar Aldehydes,Aldehydes,
ketonesketones
CarboxylCarboxyl --COOH polar, acidic, involved Amino acids,COOH polar, acidic, involved Amino acids,
in Peptide bondin Peptide bond fatty acidsfatty acids
----------------------------------------------------------------------------------------------------------------------------------------------------------
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ContinuationContinuation
----------------------------------------------------------------------------------------------------AminoAmino --NHNH22 polar,polar, basic,basic, involvedinvolved AminoAmino acidsacidsinin peptidepeptide bondbond nucleicnucleic acidsacids
PhosphatesPhosphates --POPO44 polar,polar, acidic,acidic, linkslinks NucleicNucleic acidsacids
nucleotidesnucleotides inin nucleicnucleic phospholipidsphospholipidsacidsacids
SulfhydrylSulfhydryl --SHSH formsforms disulfidedisulfide bondsbonds ThiolsThiols,,
inin somesome aminoamino acidsacids rubbersrubbers--------------------------------------------------------------------------------------------------------------------------------------------------------------------
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SynthesisSynthesis andand BreakdownBreakdown ofof
BiologicalBiological MoleculesMolecules::
Dehydration SynthesisDehydration Synthesis
-- removal ofremoval of --OH andOH and HHduring the equivalentduring the equivalentservices of a water molecule,services of a water molecule,
synthesis of a new molecule.synthesis of a new molecule.
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HydrolysisHydrolysis
-- the addition of a waterthe addition of a water
molecule to break downmolecule to break down
polymers.polymers.
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Types of MacromoleculesTypes of Macromolecules
1.)1.) CarbohydratesCarbohydrates-- containscontains carbon,carbon, oxygenoxygen andand
hydrogenhydrogen inin thethe generalgeneral formulaformula(CH(CH22O)O)nn
-- CC HH bondsbonds holdhold muchmuchenergyenergy thusthus carbohydratescarbohydrates areare goodgoodenergyenergy storagestorage moleculesmolecules
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GlycosidicGlycosidic BondBond
-- binds monosaccharidesbinds monosaccharidestogether.together.
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FU N CT I O NS :FU N CT I O NS :
important energy sourceimportant energy source(e.g. glucose)(e.g. glucose)
principal sugar transportedprincipal sugar transported
throughout bodies of land plantsthroughout bodies of land plants(e.g. sucrose)(e.g. sucrose)
energy storage (e.g. glycogen inenergy storage (e.g. glycogen inanimals; starch in plants)animals; starch in plants)
structural materialstructural material
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Types of Carbohydrates :Types of Carbohydrates :
a.)a.) MonosaccharidesMonosaccharides
-- a simple sugar consisting of3a simple sugar consisting of3to 7 carbon atomsto 7 carbon atoms
(e.g. glucose, fructose,(e.g. glucose, fructose,
galactose)galactose)
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b.)b.) DisaccharidesDisaccharides
-- aa sugarsugar consistingconsisting ofof 22monosaccharidesmonosaccharides thatthat havehave beenbeen
joinedjoined byby dehydrationdehydration synthesissynthesis..
ExampleExample::
MaltoseMaltose (glucose(glucose ++ glucose)glucose)
SucroseSucrose (glucose(glucose ++ fructose)fructose)LactoseLactose (glucose(glucose ++ galactose)galactose)
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c.)c.) OligosaccharidesOligosaccharides
-- aa sugarsugar whichwhich usuallyusually consistconsistbetweenbetween 33 toto 1010 monosaccharidemonosaccharide unitsunits..
ExampleExample::
stachyosestachyose
raffinoseraffinose
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d.) Polysaccharidesd.) Polysaccharides
-- polymerspolymers consistingconsisting ofof veryverylonglong chainschains ofof monosaccharidesmonosaccharides thatthat
areare joinedjoined byby dehydrationdehydration synthesissynthesis..
--usedused forfor energyenergy storagestorage
(plants(plants useuse starchstarch; ; animalsanimals useuseglycogen)glycogen)
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-- alsoalso usedused forfor structuralstructural
supportsupport (cellulose(cellulose inin plantsplants;; chitinchitin ininanimals)animals)
ExamplesExamples::
cellulosecellulose
starchstarch
chitinchitin
glycogenglycogen
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2.) Proteins2.) Proteins
-- composedcomposed ofof oneone oror moremore longlong
chainschains ofof aminoamino acidsacids linkedlinked byby peptidepeptide
bondsbonds..
-- havehave C,C, H,H, O,O, NN andand sometimessometimes
SS inin theirtheir moleculesmolecules
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-- thethe buildingbuilding blocksblocks ofofproteinsproteins areare aminoamino acids,acids, whichwhichcontaincontain anan aminoamino groupgroup ((--NHNH
22),), aa
carboxylcarboxyl groupgroup ((--COOH)COOH) andand aahydrogenhydrogen atom,atom, allall bondedbonded toto aa centralcentral
carboncarbon atomatom
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Cont.
-- aa peptidepeptide bondbond (covalent(covalentbond)bond) joinsjoins twotwo aminoamino acidsacids togethertogetherinin aa proteinprotein byby linkinglinking anan aminoaminogroupgroup ofof oneone aminoamino acidacid andand aacarboxylcarboxyl groupgroup ofof thethe secondsecond aminoamino
acidacid..
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2020 BiologicallyBiologically ImportantImportant AminoAmino AcidsAcids
______________________________________________________________________________
MethionineMethionine ValineValine ThreonineThreonineIsoleucineIsoleucine PhenylalaninePhenylalanine
LeucineLeucine LysineLysine CysteineCysteineTryptophanTryptophan AlanineAlanine GlycineGlycineAsparagineAsparagine AsparticAspartic AcidAcid
GlutamicGlutamic AcidAcid GlutamineGlutamine ProlineProlineSerineSerine HistidineHistidine ArginineArginine
TyrosineTyrosine
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FunctionsFunctions::
defense (e.g. antibodies,defense (e.g. antibodies,snake venom)snake venom)
transport (e.g. hemoglobin,transport (e.g. hemoglobin,myoglobin, cytochrome)myoglobin, cytochrome)
support/structural (e.g.support/structural (e.g.
collagen, keratin, fibrin)collagen, keratin, fibrin)motion (e.g. actin, myosin)motion (e.g. actin, myosin)
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Functions:
regulation (e.g. insulin,regulation (e.g. insulin,vasopressin, oxytocin)vasopressin, oxytocin)
storage (e.g. casein,storage (e.g. casein,
calmodulin)calmodulin)
enzyme catalysis (e.g.enzyme catalysis (e.g.
hydrolytic enzymes,hydrolytic enzymes,proteases, kinases)proteases, kinases)
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Protein Structure:
11..)) PrimaryPrimary structurestructure specificspecific aminoaminoacidacid sequencesequence thatthat makemake upup aa proteinprotein andand
usuallyusually assumesassumes aa linearlinear formform..
22..)) SecondarySecondary structurestructure repeatedrepeatedregularregular structurestructure assumedassumed byby proteinprotein
chainschains producedproduced byby HH bondingbonding betweenbetween
thethe atomsatoms ofof thethe polypeptidepolypeptide backbonebackbone..
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2Types ofSecondaryStructure:2Types ofSecondaryStructure:
aa..)) HelixHelix spiralspiral shapeshape isis duedue toto thethe HHbondingbonding everyevery fourthfourth aminoamino acidacid
bb..)) PleatedPleated SheathSheath resultsresults whenwhen aa
polypeptidepolypeptide turnsturns backback uponupon itselfitself andand HH
bondingbonding occursoccurs betweenbetween extendedextended lengthslengthsofof thethe polypeptidepolypeptide..
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Protein Structure:Protein Structure:
33..)) TertiaryTertiary structurestructure finalfinal foldedfoldedshapeshape ofof globularglobular proteinprotein
44..)) QuartenaryQuartenary structurestructure formsforms
whenwhen twotwo oror moremore polypeptidepolypeptide chainschains
associateassociate toto formform aa functionalfunctional proteinprotein
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Examples:Examples:
SucraseSucrase degrades sucrosedegrades sucrose
LactaseLactase degrades lactosedegrades lactose
MaltaseMaltase degrades maltosedegrades maltose
PhosphatasePhosphatase removesremovesphosphate group from itsphosphate group from its
substratesubstrate
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EnzymeStructureEnzymeStructure
-- determinesdetermines thethe enzymesenzymes particularparticular
functionfunction.. EnzymesEnzymes havehave oneone oror moremore lociloci
calledcalled activeactive sitessites toto whichwhich thethe substratessubstrates
attachesattaches..EnzymeEnzyme SpecificitySpecificity
-- enzymesenzymes areare usuallyusually specific,specific, ororuniqueunique toto thethe reactionsreactions theythey catalyzecatalyzeandand thethe substratessubstrates theythey areare involvedinvolved
inin thesethese reactionsreactions..
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Models ofEnzyme ActionModels ofEnzyme Action
Lock an Key ModelLock an Key Model-- assumesassumes thatthat thethe bindingbinding
sitesite ofof thethe enzymeenzyme hashas aa particularparticularshapeshape intointo whichwhich thethe substrate(s)substrate(s) fitfitexactlyexactly..
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Models ofEnzyme ActionModels ofEnzyme Action
Induced Fit ModelInduced Fit Model--assumes that the active siteassumes that the active site
of an enzyme can be modified as theof an enzyme can be modified as the
substrate interacts with the enzyme,substrate interacts with the enzyme,creating an induced fit betweencreating an induced fit between
enzyme and substrate.enzyme and substrate.
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33..)) NucleicNucleic AcidsAcids
-- madeup ofmadeup of
polynucleotidepolynucleotide
chains which arechains which areformed by manyformed by many
nucleotidesnucleotides, the, the
building blocks ofbuilding blocks of
nucleic acids.nucleic acids.
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-- areare formedformed whenwhen thethephosphatephosphate groupgroup of of oneone
nucleotidenucleotide isis covalentlycovalently bondedbonded
withwith thethe hydroxylhydroxyl groupgroup ofof thethesugarsugar of of another another nucleotidenucleotide
formingforming aa phosphodiesterphosphodiester bondbond..
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Components ofa NucleotideComponents ofa Nucleotide
1. 5 Csugar (pentose1. 5 Csugar (pentose
sugar)sugar)
2. phosphate group2. phosphate group3. nitrogenous bases3. nitrogenous bases
TYPES OF NITROGENOUS BASESTYPES OF NITROGENOUS BASES
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TYPES OF NITROGENOUS BASESTYPES OF NITROGENOUS BASES
a.) pyrimidine bases
- small, single ringed
molecule
1.) cytosine (C)2.) thymine (T) in DNA;
uracil (U) in RNA
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TYPESTYPES OFOF NITROGENOUSNITROGENOUS BASESBASES
bb..)) purinepurine basesbases
-- large,large, doubledouble ringedringed
moleculemolecule11..)) guanineguanine (G)(G)
22..)) adenineadenine (A)(A)
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NucleotideNucleotide
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TwoTwoClassesClasses ofofNucleicNucleic AcidsAcids
1.) Deoxyribonucleic Acid(DNA)
- found in all living things
- encodes information
used to assemble
proteins
- has a deoxyribose sugar
and has thymine as one of
the pyrimidinebases
D ib l i A id (DNA)
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Deoxyribonucleic Acid (DNA)
________________________________-- double strandeddouble stranded
(composed of two(composed of two
strands held togetherstrands held togetherby H bonds)by H bonds)
-- the two strands arethe two strands are
twisted around eachtwisted around each
other forming a doubleother forming a double
helixhelix
D ib l i A id (DNA)
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Deoxyribonucleic Acid (DNA)
________________________________
-- the double helicalthe double helical
structure of DNA wasstructure of DNA was
proposed byproposed by JamesJames
WatsonWatson andand FrancisFrancis
CrickCrick in 1950in 1950
-- primarily found in theprimarily found in thenucleus but also presentnucleus but also present
in mitochondria andin mitochondria and
chloroplastschloroplasts
Deoxyribonucleic Acid (DNA)
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Deoxyribonucleic Acid (DNA)
________________________________-- pairingpairing ofof nitrogenousnitrogenousbasesbases isis specificspecific..
SpecificSpecific purinespurines alwaysalways
pairpair withwith specificspecificpyrimidinespyrimidines
(complementary(complementary basebase
pairing)pairing)
AA == TT (bonded(bonded byby 22 HH bonds)bonds)
GG == CC (bonded(bonded byby 33 HH bonds)bonds)
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2.) Ribonucleic Acid (RNA)2.) Ribonucleic Acid (RNA)
________________________________________________________________-- carriescarries thethe geneticgenetic codecode
intointo thethe cytoplasmcytoplasm
-- directsdirects thethe synthesissynthesis ofof
proteinsproteins
-- singlesingle--strandedstranded-- contains ribose sugarcontains ribose sugar
instead of deoxyriboseinstead of deoxyribose
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Ribonucleic Acid (RNA)Ribonucleic Acid (RNA)
________________________________________________________________
-- containscontains uraciluracil (U) in(U) in
place of thymine (T)place of thymine (T)
RNA NitrogenousRNA Nitrogenous
PairingPairing
A = UA = U
G = CG = C
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Kinds ofRNAKinds ofRNA
______________________________________________________________________
1.)1.)messenger RNA (mRNA)messenger RNA (mRNA)
-- carriescarries thethe DNAsDNAs geneticgenetic
codecode toto thethe r ibosomeribosome forfortranslationtranslation..
22..))transfertransfer RNARNA ((tRNAtRNA))
-- bringsbrings aminoamino acidsacids toto
ribosomeribosome forfor proteinprotein synthesissynthesis
ff
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Kinds ofRNAKinds ofRNA
________________________________________________________________
3.)3.)ribosomal RNA (ribosomal RNA (rRNArRNA))
-- structuralstructuralcomponent ofthecomponent ofthe
ribosomesribosomes
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OtherOther kindskinds ofof NucleotidesNucleotides
________________________________________________________________1.) Cyclic Nucleotides1.) Cyclic Nucleotides
-- carry informationfromcarry informationfrom
the cell membrane tothe cell membrane toother molecules in theother molecules in the
cellcell
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Otherkinds ofNucleotidesOtherkinds ofNucleotides
________________________________________________________________2.)2.) DiphosphateDiphosphateandand
TriphosphateTriphosphate NucleotidesNucleotides
-- highenergy moleculeshighenergy molecules
that carry energy tothat carry energy to
different parts ofthedifferent parts ofthecell.cell.
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Example:Example:
1.) ADP (adenosine1.) ADP (adenosine
diphospatediphospate))
2.) ATP (adenosine2.) ATP (adenosinetriphosphatetriphosphate))
-- considered as theconsidered as the
energy currency ofenergy currency of
the cellthe cell
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4.) Lipids4.) Lipids
-- looselyloosely defineddefined asasgroupsgroups ofof moleculesmolecules thatthat areare
insolubleinsoluble inin waterwater
-- primarilyprimarily composedcomposed ofof
C,C, H,H, OO andand othersothers havehave PP andand NN
-- storestore twicetwice asas muchmuchenergyenergy asas carbohydratescarbohydrates
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F tF t ii
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Fu c tFu c t ii o n :o n :
-- energyenergy storagestorage
-- protection andprotection and
cushioning of bodycushioning of body
organsorgans-- structural componentsstructural components
of membranesof membranes
-- chemical messengerschemical messengers
(hormones)(hormones)
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Components of LipidsComponents of Lipids