lect8 chemistry 2011

8/3/2019 Lect8 Chemistry 2011

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LECTURE 8:LECTURE 8:

CHEMISTRY OF LIFECHEMISTRY OF LIFE

Botany scientific study of plant life

Teaching Philosophy

"Give a man a fish, and he will eat for a day, but teach a manto fish and he will eat for a lifetime" - Confucius.

Limonene (L-limonene & D-limonene)

http://waynesword.palomar.edu/chemid1.htm#carbohydrates

Welcome to my lectureWelcome to my lectureWho am I ?: Prof. Dr. S.M.Who am I ?: Prof. Dr. S.M. SitompulSitompul

These are my rulesThese are my rules

I always come on timeI always come on time(( 10) with a proper10) with a properdressdress

Get into the lectureGet into the lectureroom, dont hangroom, dont hangaroundaround

I use English in myI use English in mylecture and exam (25lecture and exam (25--75%)75%)

These are my philosophies

Turn your enemies to beyour friends

Turn your useless timeto be useful time

Make big problems to besmall problems

Simplify the systems orproblems

PREPARATIONPREPARATION My DictionaryMy Dictionary

Buy a writing book (100 pages)Buy a writing book (100 pages)write the title write the title MyMyDictionaryDictionary

Write every word that you do not understand in myWrite every word that you do not understand in mylecture and from others, and get the meaning of it (youlecture and from others, and get the meaning of it (you

have to show this at the end of my lecture)have to show this at the end of my lecture) you toyou tohave at least 100 wordshave at least 100 words

English PresentationEnglish Presentation Everyone has to make English Presentation (EP)Everyone has to make English Presentation (EP)

The EP is started from the English judgesThe EP is started from the English judges

The English judges have to coordinate their friends forThe English judges have to coordinate their friends forthe EP and take marksthe EP and take marks

SelfSelf--Propagating GroupsPropagating Groups Form groups with 5 members eachForm groups with 5 members each

Discuss lecture materials in your groupsDiscuss lecture materials in your groups

LECTURE FLOWLECTURE FLOWI. INTRODUCTIONI. INTRODUCTION

1.1. DefinitionDefinition

2.2. ApproachApproach

3.3. LifeLife

4.4. Biology SystemsBiology Systems

5.5. CELLCELL

II. CHEMISTRY AND LIFEII. CHEMISTRY AND LIFE

1.1. Atom and Atom StructureAtom and Atom Structure

2.2. Organic Compounds of PlantsOrganic Compounds of Plants

III.III. MOLECULE FORMATION

1. Atom Characteristics2. Covalent and Ionic Bond


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I. INTRODUCTIONI. INTRODUCTION

1. Definition1. Definition Botany can be defined asBotany can be defined as thethe scientificscientific

study of plant lifestudy of plant life..

The study ofThe study of lifelife isis biologybiology, and the word, and the wordbiology is composed of 2 Greek roots biobiology is composed of 2 Greek roots biowhich mean life, and which mean life, and logilogi which means which meansstudy ofstudy of

Biology as a science is concerned withBiology as a science is concerned with allalllifelife-- plant and animal,plant and animal, but botany isbut botany isinterestedinterested in plant life in particularin plant life in particular..

To Understand the Big, Youd Better Know the Small

Our journey begins here.

Simple to ComplexSimple to Complex Lifes Levels of OrganizationLifes Levels of Organization

2. Approach

INTRODUCTIONINTRODUCTION

3. Life3. Life

As Botany =As Botany = study of plant life, then whatstudy of plant life, then whatis life?is life?

If we were to list the criteria for definingIf we were to list the criteria for defininglife what would they be?life what would they be? All living things are composed of cellsAll living things are composed of cells

They have self regulating metabolismsThey have self regulating metabolisms

They moveThey move

Respond to stimuliRespond to stimuli

ReproduceReproduce

Adapt to environmentAdapt to environment

INTRODUCTIONINTRODUCTION INTRODUCTIONINTRODUCTION

Plant life meansPlant life means1.1. OrganizationOrganization: Being composed of one: Being composed of one

or more Cells, which are the basic units ofor more Cells, which are the basic units oflife.life.

2.2. MetabolismMetabolism : Consumption of energy by: Consumption of energy byconverting nonliving material into cellularconverting nonliving material into cellularcomponents (anabolism) andcomponents (anabolism) anddecomposing organic matter (catabolism)decomposing organic matter (catabolism)

3.3. GrowthGrowth:: Maintenance of a higher rate ofMaintenance of a higher rate ofsynthesis than catalysissynthesis than catalysis


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4.4. AdaptationAdaptation: The ability to change over a period: The ability to change over a periodof time in response to the environmentof time in response to the environment

5.5. ReproductionReproduction: The ability to produce new: The ability to produce neworganisms (the production of new cells in theorganisms (the production of new cells in theprocess of growth )process of growth )

Botany covers the study ofBotany covers the study of::Structure, growth, reproduction, development,Structure, growth, reproduction, development,metabolism, diseases, and chemical properties ofmetabolism, diseases, and chemical properties ofover 550,000 kinds or species of living organismsover 550,000 kinds or species of living organisms

including plants, algae, viruses, bacteria and fungiincluding plants, algae, viruses, bacteria and fungi

Historically, botany covers all organisms thatHistorically, botany covers all organisms thatwere not considered to be animalswere not considered to be animals

Some of these organisms are:Some of these organisms are: PlantsPlants PlantPlant--like organismslike organisms

include fungi, (studied in mycology), bacteria , andinclude fungi, (studied in mycology), bacteria , andviruses (studied in microbiology), and algae (studiedviruses (studied in microbiology), and algae (studiedinin phycologyphycology).).

The study of plants has importance for aThe study of plants has importance for anumber of reasons:number of reasons:1.1. Plants has a fundamental part of life on Earth.Plants has a fundamental part of life on Earth.2.2. They generate the oxygen, food, fibers, fuel andThey generate the oxygen, food, fibers, fuel and

medicine that allow higher life forms to exist.medicine that allow higher life forms to exist.3.3. Plants also absorb carbon dioxide throughPlants also absorb carbon dioxide through

photosynthesis, that in large amounts can effectphotosynthesis, that in large amounts can effectglobal climate.global climate.

44. Biology Systems. Biology Systems

Biology organizes living thingsBiology organizes living thingsalong certain levels.along certain levels. at aat a chemical levelchemical level, looking at the, looking at the

biochemistry of organisms, orbiochemistry of organisms, or

at aat a cellular levelcellular level where interest in thewhere interest in thestructure and functions of cells and cellstructure and functions of cells and cellphysiology is considered, orphysiology is considered, or

at theat the levels of tissues or organslevels of tissues or organs..

5. CELL5. CELL All life begins in one cell which consists ofAll life begins in one cell which consists of

organellesorganelles Organelles consist of moleculesOrganelles consist of molecules Molecules consist of chemical elementsMolecules consist of chemical elements chemistry of lifechemistry of life

TheThe CELLCELL is the smallest unit of livingis the smallest unit of livingmatter. The smallest living things are onematter. The smallest living things are onecelled animals (certain bacteria and algae)celled animals (certain bacteria and algae)

Larger organisms are collections of cells inLarger organisms are collections of cells inwhich cells are differentiated by function bywhich cells are differentiated by function byact in concert, that is they are organized andact in concert, that is they are organized andcooperate.cooperate.


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Cells are the basic and fundamentalCells are the basic and fundamental

unit of structure, physiology, andunit of structure, physiology, andorganization of all living organisms.organization of all living organisms.

Knowing the composition of cells andKnowing the composition of cells andhow cells work is fundamental to allhow cells work is fundamental to allof the biological sciencesof the biological sciences

II. Chemical Compounds In PlantsII. Chemical Compounds In Plants

1.1. The chemical basis of lifeThe chemical basis of life

Life is a chemical processLife is a chemical process. All aspects. All aspectsof living creatures have a chemicalof living creatures have a chemicalbasis.basis.

An understanding of life requires anAn understanding of life requires anunderstanding ofunderstanding of the chemical basisthe chemical basisof lifeof life..

Chemistry is the study ofChemistry is the study of the properties ofthe properties ofmattermatter

The fundamental unit of matter is theThe fundamental unit of matter is the atomatom..Everything that hasEverything that has massmass andand occupies spaceoccupies space

is composed ofis composed of atomsatoms oror subatomic particlessubatomic particles..

Living systems can be organized into theLiving systems can be organized into thefollowing levels or categoriesfollowing levels or categories1.1. Subatomic particlesSubatomic particles ((electrons, protons and neutrons)electrons, protons and neutrons)

formform

2.2. atomsatoms (hydrogen, helium, oxygen, iron, etc.) which(hydrogen, helium, oxygen, iron, etc.) which

form molecules (water, glucose, cellulose, etc.) whichform molecules (water, glucose, cellulose, etc.) whichformform

3.3. complex macromoleculescomplex macromolecules ((glycoproteinsglycoproteins, DNA, RNA,, DNA, RNA,etc.) which formetc.) which form

4.4. subcellularsubcellular unitsunits called organelles (nucleus,called organelles (nucleus,mitochondrion, chloroplast, etc.) which formmitochondrion, chloroplast, etc.) which form

5.5. cellscells which form tissues (muscle, nerve, adipose,which form tissues (muscle, nerve, adipose,

epithelial, etc.) which formepithelial, etc.) which form

6.6. organsorgans (brain, heart, liver, root, leaf, etc.) which form(brain, heart, liver, root, leaf, etc.) which form7.7. an individual organisman individual organism

2. Atoms and Atomic Structure Atomic Nucleus contains Protons and

Neutrons Neutrons and Protons have similar mass

(weight)

Electrons have a verysmall mass and spinaround the AtomicNucleus

Atoms have equalnumber of protons (+)and electrons (-)


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2.2. Organic Compounds of PlantsOrganic Compounds of Plants The major groups of organic compounds as farThe major groups of organic compounds as far

as life is concerned are:as life is concerned are:

Hydrogen, oxygen and nitrogen are frequentlyHydrogen, oxygen and nitrogen are frequentlyfound bonded to carbon. Organic compoundsfound bonded to carbon. Organic compoundsmade up of carbon and hydrogen are known asmade up of carbon and hydrogen are known ashydrocarbonshydrocarbons,, this includes what commonthis includes what commonmaterials?materials?

1. Carbohydrates 5. Terpenes

2. Lipids 6. Phenolic Compounds

3. Proteins 7. Glycosides

4. Nucleic Acids 8. Alkaloids

http://waynesword.palomar.edu/chemid1.htm#carbohydrates

III. MOLECULE FORMATIONIII. MOLECULE FORMATION

1.1. Atom CharacteristicsAtom Characteristics The molecular constituent of plants are synthesizedThe molecular constituent of plants are synthesized

from far simple, inorganic molecules (from far simple, inorganic molecules (COCO22, H, H22O andO andnutrient elementsnutrient elements))

What causes atoms to form molecules?

The formation ofThe formation ofalmost all livingalmost all livingmolecules occurmolecules occurthroughthrough reactionsreactionscatalyzed bycatalyzed byenzymesenzymes andand basedbasedon characteristicson characteristics ofofbasic constituent ofbasic constituent ofthe moleculesthe molecules

(atom)(atom)

In a simplified yet useful view of an atom,electrons orbit a nucleus composed of

protons and neutrons.

Atoms come in different forms called isotopesAtoms come in different forms called isotopes1.1. Isotopes of a given element have the sameIsotopes of a given element have the same

number of protons but different numbers ofnumber of protons but different numbers ofneutrons.neutrons.

2.2. Many isotopes are unstable, making themMany isotopes are unstable, making themradioactive.radioactive.

3.3. Radioactive isotopes (radioisotopes) play anRadioactive isotopes (radioisotopes) play an

important role in health, medicine andimportant role in health, medicine and biologicalbiologicalresearch.research.

Three isotopes of hydrogen.


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Some Atoms are Sociable, Others Arent Atoms want (are most stable) to have a filled outer electron

shell.

Atoms without a filled outer shell will share electronswith other atoms to accomplish this goal.

Filling outerelectron shellscontrols whichatom will pairwith which othersand in whatcombinations.

Filling Electron Shells

An important rule:

the innermost shell holds

two electrons; subsequent shells hold 8

electrons.

Pairing for the Greater Good

2. Molecule Formation There are two types of bonds that can form between

atoms: covalent bond & ionic bond When atoms come together by sharing electrons

the bond is a covalent bond.

H2

A molecule is

formed when two or

more atoms arebound together

covalently.

Water (H2O) - A Most Important Molecule

Note how bonding fills all outer electron shells.


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Valence ElectronsValence Electrons The electrons found in the outer shell of anThe electrons found in the outer shell of an

atom are known asatom are known as valence electronsvalence electrons The valence of an atom isThe valence of an atom is the number ofthe number of

electrons an atom must receive to becomeelectrons an atom must receive to becomechemically stablechemically stable (i.e., less reactive)(i.e., less reactive)

For many atoms Valence = 8For many atoms Valence = 8 -- # valence# valenceelectronselectrons OxygenOxygen: 6 valence electrons, valence = 2: 6 valence electrons, valence = 2

NitrogenNitrogen: 5 valence electrons, valence = 3: 5 valence electrons, valence = 3

CarbonCarbon: 4 valence electrons, valence = 4: 4 valence electrons, valence = 4

In BiologyIn Biology (even in chemistry)(even in chemistry) there arethere arealways exceptions:always exceptions: Hydrogen: 1 valence electron, valence = 1Hydrogen: 1 valence electron, valence = 1

Phosphorus: 5 valence electrons, valence = 5Phosphorus: 5 valence electrons, valence = 5

Valences of Various ElementsValences of Various Elements

1

4 3 2

5 1

Polar and Non-Polar Covalent Bonding

A polarsubstance is one in which the molecule hasa negative side and a positive side

The covalent bonds of H2 and CH4 are non-polar and so are the molecules.

Some atoms have an equalaffinity for electrons.If so, the shared electrons spendequal amounts of time aroundeach atom and the covalentbond is non-polar.

Polar and Non-Polar Covalent Bonding

Therefore, the covalent bonds of H2O are highly

polar and so is the molecule.

Some atoms have an unequal affinity for electrons.If so, the shared electrons spend more time around oneatom relative to another and the covalent bond is polar.

Oxygen draws electrons toitself much more stronglythan hydrogen.

H2O


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Polar and Non-Polar Covalent Bonding Polar and Non-Polar Covalent Bonding

The polar versus non-polar distinction determineswhich molecules will dissolve in a particular solute.

For example, sugar dissolves inwater, but fat doesnt.The general rule is like dissolveslike.

The familiar case of oil and waterWater = polar moleculeFat = non-polar moleculeSoap = polar and non-polar

molecule

Some Atoms Do Almost Anything to Fill Electron Shells

Sodium donates a lonely electron to chlorine to complete itsouter electron shell. Chlorine is only too happy to accept.

The result is ion formation.

An ion is an atom or molecule with one or more fullpositive or negative charges.

Ions and Ion Formation


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Ionic BondsTwo oppositely charged ions bind together.This type of chemical bond is an ionic bond.

Salts are solidsheld together byionic bonds.Ionic bonds arecommon andimportant inbiology.

Ionic bondingIonic bonding

High electronegativityHigh electronegativitydifference stripsdifference stripsvalence electronsvalence electronsaway from anotheraway from anotheratomatom

Electron transferElectron transfercreates ions (chargedcreates ions (chargedatoms)atoms)

Cation (positive ion);Cation (positive ion);anion (negative ion)anion (negative ion)

Ex: Salts (sodiumEx: Salts (sodiumchloride)chloride)

Ionic BondingIonic Bonding

Ionic bonds result fromone atom essentiallygiving an electron to

another atom

Ionic bonds represent anextreme of polarity andare represented inbiological systems as thesalt bridges within proteins

Ionic bondingIonic bondingIonic bonding involves 3 steps (3 energies)Ionic bonding involves 3 steps (3 energies)

1) loss of an electron(s) by one element,1) loss of an electron(s) by one element,2) gain of electron(s) by a second element,2) gain of electron(s) by a second element,3) attraction between positive and negative3) attraction between positive and negative

+Na e Na+Ionization energy

Cl e+ ClElectron affinity

Lattice energy

+ Cl

Na

+Cl

Na+

+Na e Na++Na e Na+NaNa e Na+Na+Ionization energy

Cl e+ ClClCl e+ e+ ClClElectron affinity

Lattice energy

+ Cl

Na

+Cl

Na+

+ Cl

Cl

Na

+

Na

+ClCl

Na+

Na+


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Ionic bonding: energiesIonic bonding: energies By convention, a requirement for energy is givenBy convention, a requirement for energy is given

a + sign (we have to put energy in) and is calleda + sign (we have to put energy in) and is calledendothermic, a release of energy is given aendothermic, a release of energy is given a signsignand is called exothermic.and is called exothermic.

+Na e Na+Ionization energy

Cl e+ ClElectron affinity

Lattice energy+ Cl Na+Cl Na+

+ 496

349

766

+NaNa e Na+Na+Ionization energy

ClCl e+ ClClElectron affinity

Lattice energy+ ClCl Na+Na+ClCl Na+Na+

+ 496

349

766

Hydrogen BondingOxygen and nitrogen are much more hungry forelectrons than hydrogen.

The result is a hydrogenbond.

Bonds between nitrogen oroxygen and hydrogen arehighly polar.This allows bonds to formbetween partially positiveand partially negativeatoms in different or (inlarge molecules) the samemolecule.

Hydrogen Bonding Gives Water UniqueProperties

lect8 chemistry 2011

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