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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