chemical foundations for cells chapter 2. chemical benefits and costs understanding of chemistry...

Chemical Chemical Foundations Foundations

for Cellsfor CellsChapter 2Chapter 2

Chemical Benefits and Chemical Benefits and CostsCosts

Understanding of chemistry Understanding of chemistry provides fertilizers, provides fertilizers, medicines, etc.medicines, etc.

Chemical pollutants damage Chemical pollutants damage ecosystemsecosystems

BioremediationBioremediation

Use of living organisms to Use of living organisms to withdraw harmful substances withdraw harmful substances

from the environmentfrom the environment

ElementsElements

Fundamental forms of matterFundamental forms of matter

Can’t be broken apart by Can’t be broken apart by

normal meansnormal means

92 occur naturally on Earth92 occur naturally on Earth

Most Common Elements Most Common Elements in Living Organismsin Living Organisms

OxygenOxygen

HydrogenHydrogen

CarbonCarbon

NitrogenNitrogen

Fig. 2.2, p. 21

What Are Atoms?What Are Atoms?

Smallest particles that retain properties Smallest particles that retain properties

of an elementof an element Made up of subatomic particles:Made up of subatomic particles:

Protons (+)Protons (+)

Electrons (-) Electrons (-)

Neutrons (no charge) Neutrons (no charge)

Fig. 2.3, p. 22

HYDROGEN HELIUM

electron

proton

neutron

Hydrogen and Helium Atoms

ProtonsProtons

Positively charged Positively charged Found in the nucleusFound in the nucleus Has a massHas a mass

NeutronsNeutrons

No chargeNo charge Found in the nucleusFound in the nucleus Has a massHas a mass

ElectronsElectrons

Negatively charged Negatively charged Constantly moving around in the Constantly moving around in the

electron cloud surrounding the electron cloud surrounding the nucleusnucleus

Negligible Mass (1/1840 the mass of Negligible Mass (1/1840 the mass of a proton)a proton)

What information does the What information does the Periodic Table of Elements Periodic Table of Elements

contain?contain?

Atomic NumberAtomic Number

Number of protonsNumber of protons All atoms of an element have the All atoms of an element have the

same atomic numbersame atomic number Atomic number of hydrogen = 1Atomic number of hydrogen = 1 Atomic number of carbon = 6Atomic number of carbon = 6

Mass NumberMass Number

Number of protonsNumber of protons

++Number of neutronsNumber of neutrons

Isotopes vary in mass numberIsotopes vary in mass number

How can we determine How can we determine the number of neutrons?the number of neutrons?

Subtract the total number of protons Subtract the total number of protons from the atomic mass. from the atomic mass.

Determine the symbol, Determine the symbol, number of protons, number of protons,

neutrons and electrons neutrons and electrons of each of the following of each of the following

elements.elements. HydrogenHydrogen SodiumSodium OxygenOxygen IronIron

IsotopesIsotopes

Atoms of an element with different Atoms of an element with different numbers of neutrons (different mass numbers of neutrons (different mass numbers)numbers)

Carbon 12 has 6 protons, 6 neutronsCarbon 12 has 6 protons, 6 neutrons Carbon 14 has 6 protons, 8 neutronsCarbon 14 has 6 protons, 8 neutrons

RadioisotopesRadioisotopes

Have an unstable nucleus that Have an unstable nucleus that emits energy and particlesemits energy and particles

Radioactive decay transforms Radioactive decay transforms radioisotope into a different radioisotope into a different elementelement

Decay occurs at a fixed rateDecay occurs at a fixed rate

Radioisotopes as TracersRadioisotopes as Tracers

Tracer is substance with a Tracer is substance with a radioisotope attached to itradioisotope attached to it

Emissions from the tracer Emissions from the tracer can be detected with special can be detected with special devices devices

Following movement of Following movement of tracers is useful in many tracers is useful in many areas of biologyareas of biology

Thyroid ScanThyroid Scan

Measures health of thyroid by detecting Measures health of thyroid by detecting radioactive iodine taken up by thyroid radioactive iodine taken up by thyroid glandgland

normal thyroid enlarged cancerous

Other Uses of Other Uses of RadioisotopesRadioisotopes

Drive artificial pacemakersDrive artificial pacemakers

Radiation therapyRadiation therapyEmissions from some radioisotopes can Emissions from some radioisotopes can destroy cells. Some radioisotopes are destroy cells. Some radioisotopes are used to kill small cancers.used to kill small cancers.

What Determines What Determines Whether Atoms Whether Atoms Will Interact?Will Interact?

The number and arrangement of The number and arrangement of their electronstheir electrons

ElectronsElectrons

Carry a negative chargeCarry a negative charge Repel one another Repel one another Are attracted to protons Are attracted to protons

in the nucleusin the nucleus Move in orbitals - Move in orbitals -

volumes of space that volumes of space that surround the nucleussurround the nucleus

Z

X

When all p orbitals are full

y

Electron CloudElectron Cloud

Broken into different energy levels Broken into different energy levels (orbitals)(orbitals)

1st level can hold - 2 electrons1st level can hold - 2 electrons 2nd level can hold - 8 electrons2nd level can hold - 8 electrons 3rd level can hold - 18 electrons3rd level can hold - 18 electrons

sub level A holds 8 electronssub level A holds 8 electrons sub level B holds 10 electronssub level B holds 10 electrons

Every atom wants a complete Every atom wants a complete outer energy level to be as stable outer energy level to be as stable as possible.as possible.

In order to do this the atom has In order to do this the atom has three choicesthree choices donate electronsdonate electrons accept electronsaccept electrons share electronsshare electrons

Electron VacanciesElectron Vacancies

Unfilled shells Unfilled shells make atoms likely make atoms likely to reactto react

Hydrogen, Hydrogen, carbon, oxygen, carbon, oxygen, and nitrogen all and nitrogen all have vacancies in have vacancies in their outer shellstheir outer shells

CARBON6p+ , 6e-

NITROGEN7p+ , 7e-

HYDROGEN1p+ , 1e-

Draw models of the Draw models of the following atoms. following atoms.

Include the number Include the number of protons, of protons,

neutrons and neutrons and electons.electons.

Helium, Carbon, OxygenHelium, Carbon, Oxygen

Important Bonds Important Bonds in Biological in Biological

MoleculesMoleculesIonic BondsIonic Bonds

Covalent BondsCovalent Bonds

Hydrogen BondsHydrogen Bonds

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Ion FormationIon Formation

Atom has equal number of Atom has equal number of electrons and protons - no net electrons and protons - no net chargecharge

Atom loses electron(s), becomes Atom loses electron(s), becomes positively charged ionpositively charged ion

Atom gains electron(s), becomes Atom gains electron(s), becomes negatively charged ionnegatively charged ion

Ionic BondingIonic Bonding

One atom loses electrons, One atom loses electrons, becomes positively charged becomes positively charged ionion

Another atom gains these Another atom gains these electrons, becomes electrons, becomes negatively charged ionnegatively charged ion

Charge difference attracts Charge difference attracts the two ions to each otherthe two ions to each other

Formation of NaClFormation of NaCl

Sodium atom (Na) Sodium atom (Na) Outer shell has one electronOuter shell has one electron

Chlorine atom (Cl) Chlorine atom (Cl) Outer shell has seven electronsOuter shell has seven electrons

Na transfers electron to Cl forming Na transfers electron to Cl forming NaNa++ and Cland Cl--

Ions remain together as NaClIons remain together as NaCl

7mm

SODIUMATOM11 p+

11 e-

SODIUMION

11 p+

10 e-

electron transfer

CHLORINEATOM17 p+

17 e-

CHLORINEION

17 p+

18 e-

Fig. 2.10a, p. 26

Formation of NaCl

Ionic Bonding PracticeIonic Bonding Practice

Show how the following compounds Show how the following compounds form as a result of ionic bondingform as a result of ionic bonding

NaF - Sodium FlourideNaF - Sodium Flouride MgO - Magnesium OxideMgO - Magnesium Oxide LiLi22S - Lithium SulfideS - Lithium Sulfide

Covalent BondingCovalent Bonding

Atoms share a pair or pairs of electrons Atoms share a pair or pairs of electrons to fill outermost shellto fill outermost shell

•Single covalent bond

•Double covalent bond

•Triple covalent bond

Covalent Bonds

Covalent Bonding Covalent Bonding PracticePractice

Show how the following compounds Show how the following compounds form as a result of ionic bondingform as a result of ionic bonding

HH22S - Hydrogen SulfideS - Hydrogen Sulfide

NHNH33 - Nitrogen Trihydride - Nitrogen Trihydride (Ammonia)(Ammonia)

FF22 - Diatomic Fluorine - Diatomic Fluorine

Nonpolar Covalent BondsNonpolar Covalent Bonds

Atoms share electrons equallyAtoms share electrons equally

Nuclei of atoms have same Nuclei of atoms have same number of protonsnumber of protons

Example: Hydrogen gas (H-Example: Hydrogen gas (H-H)H)

Polar Covalent BondsPolar Covalent Bonds

Number of protons in nuclei of Number of protons in nuclei of participating atoms is NOT equalparticipating atoms is NOT equal

Electrons spend more time near Electrons spend more time near nucleus with most protonsnucleus with most protons

Water - Electrons more attracted Water - Electrons more attracted to O nucleus than to H nucleito O nucleus than to H nuclei

Polar BondingPolar Bonding

During covalent bonding the sharing of electrons is not always equal. This unequal sharing leads to slightly positive and negative regions.

Hydrogen BondingHydrogen Bonding

Molecule held together by polar covalent Molecule held together by polar covalent bonds has no NET charge bonds has no NET charge

However, atoms of the molecule carry However, atoms of the molecule carry different chargesdifferent charges

Atom in one polar covalent molecule can Atom in one polar covalent molecule can be attracted to oppositely charged atom in be attracted to oppositely charged atom in another such moleculeanother such molecule

onelargemolecule

anotherlargemolecule

a largemoleculetwistedbackonitself Fig. 2.12, p. 27

Examples of Hydrogen Bonds

Chemical Bonds, Chemical Bonds, Molecules, Molecules,

& Compounds& Compounds Bond is union between electron Bond is union between electron

structures of atomsstructures of atoms Atoms bond to form moleculesAtoms bond to form molecules Molecules may contain atoms of only Molecules may contain atoms of only

one element - Oone element - O22

Molecules of compounds contain Molecules of compounds contain more than one element - Hmore than one element - H22OO

Chemical BookkeepingChemical Bookkeeping

Use symbols for elements when Use symbols for elements when writing formulaswriting formulas

Formula for glucose is CFormula for glucose is C66HH1212OO66

6 carbons 6 carbons

12 hydrogens12 hydrogens

6 oxygens6 oxygens

Chemical BookkeepingChemical Bookkeeping

Chemical equation shows reactionChemical equation shows reactionReactants ---> ProductsReactants ---> Products

Equation for photosynthesis:Equation for photosynthesis:

6CO6CO22 + 6H + 6H22O ---> + CO ---> + C66HH1212OO66 + 6H + 6H22OO

REACTANTS PRODUCTS

6CO2

CARBONDIOXIDE

12H2O

WATER

+ C6H12O6

GLUCOSE

6H2O

WATER

+

6 carbons12 oxygens

24 hydrogens12 oxygens

6 carbons12 hydrogens

6 oxygens

12 hydrogens6 oxygens

Fig. 2.9, p. 25

6O2

OXYGEN

+

12 oxygens

sunlightenergy

ReactantsReactants

The elements or compounds that The elements or compounds that enter into a chemical reactionenter into a chemical reaction

ProductProduct

The elements or compounds The elements or compounds produced by a chemical reactionproduced by a chemical reaction

Energy in Energy in ReactionsReactions

What is Energy?What is Energy?

Capacity to do workCapacity to do work

Forms of energyForms of energy Potential energyPotential energy Kinetic energyKinetic energy Chemical energyChemical energy

What Can Cells Do What Can Cells Do with Energy?with Energy?

Energy inputs become coupled Energy inputs become coupled

to energy-requiring processesto energy-requiring processes

Cells use energy for:Cells use energy for: Chemical workChemical work

Mechanical workMechanical work

Electrochemical workElectrochemical work

First Law of First Law of ThermodynamicsThermodynamics

The total amount of energy in the The total amount of energy in the universe remains constantuniverse remains constant

Energy can undergo conversions Energy can undergo conversions from one form to another, but it from one form to another, but it cannot be created or destroyedcannot be created or destroyed

One-Way Flow of EnergyOne-Way Flow of Energy

The sun is life’s primary energy sourceThe sun is life’s primary energy source

Producers trap energy from the sun Producers trap energy from the sun and convert it into chemical bond and convert it into chemical bond energyenergy

AllAll organisms use the energy stored in organisms use the energy stored in the bonds of organic compounds to do the bonds of organic compounds to do work work

Second Law of Second Law of ThermodynamicsThermodynamics

No energy conversion is ever 100 No energy conversion is ever 100

percent efficientpercent efficient

The total amount of energy is The total amount of energy is

flowing from high-energy forms to flowing from high-energy forms to

forms lower in energyforms lower in energy

Energy Changes & Energy Changes & Cellular WorkCellular Work

Energy changes in cells tend to Energy changes in cells tend to run spontaneously in the direction run spontaneously in the direction that results in a decrease in usable that results in a decrease in usable

energyenergy

Endergonic ReactionsEndergonic Reactions Energy input requiredEnergy input required

Product has more Product has more

energy than starting energy than starting

substancessubstances

product withmore energy

(plus by-products602 and 6H2O)

ENERGY IN

6 12

Exergonic ReactionsExergonic Reactions

Energy is Energy is releasedreleased

Products have Products have less energy less energy than starting than starting substancesubstance

ENERGY OUT

energy-richstarting

substance

+602

products with less energy

6 6

Properties of Properties of WaterWater

PolarityPolarity

Temperature-StabilizingTemperature-Stabilizing

CohesiveCohesive

SolventSolvent

Water Is a Polar Water Is a Polar Covalent MoleculeCovalent Molecule

Molecule has no net Molecule has no net chargecharge

Oxygen end has a Oxygen end has a slight negative slight negative chargecharge

Hydrogen end has a Hydrogen end has a slight positive chargeslight positive charge

O

H H

O

H

HO

H

H

+ _

++

+

_

+

+

Liquid Water

Surface TensionSurface Tension

The cohesive nature of water allows The cohesive nature of water allows it to overcome the density of objects.it to overcome the density of objects.

DemonstrationDemonstration

Allows for water walking insects and Allows for water walking insects and lizards.lizards.

EXPLAIN….EXPLAIN….Using Scientific principles, terminology, critical thinking, Using Scientific principles, terminology, critical thinking, to explain what this photo represents..to explain what this photo represents..

Hydrophilic & Hydrophilic & HydrophobicHydrophobicSubstancesSubstances

Hydrophilic substancesHydrophilic substances PolarPolar Hydrogen bond with water Hydrogen bond with water Example: sugarExample: sugar

Hydrophobic substancesHydrophobic substances NonpolarNonpolar Repelled by waterRepelled by water Example: oilExample: oil

Temperature-Stabilizing Temperature-Stabilizing EffectsEffects

Liquid water can absorb much Liquid water can absorb much heat before its temperature risesheat before its temperature rises

Why? Why?

Much of the added energy Much of the added energy disrupts hydrogen bonding rather disrupts hydrogen bonding rather than increasing the movement of than increasing the movement of moleculesmolecules

Evaporation of WaterEvaporation of Water

Large energy input can cause individual Large energy input can cause individual molecules of water to break free into airmolecules of water to break free into air

As molecules break free, they carry As molecules break free, they carry away some energy (lower temperature)away some energy (lower temperature)

Evaporative water loss is used by Evaporative water loss is used by mammals to lower body temperaturemammals to lower body temperature

Why Ice FloatsWhy Ice Floats

In ice, hydrogen bonds lock In ice, hydrogen bonds lock molecules in a lattice molecules in a lattice

Water molecules in lattice are Water molecules in lattice are spaced farther apart then those in spaced farther apart then those in liquid waterliquid water

Ice is less dense than waterIce is less dense than water

Water CohesionWater Cohesion

Hydrogen bonding holds Hydrogen bonding holds molecules in liquid water molecules in liquid water togethertogether

Creates surface tension Creates surface tension

Allows water to move as Allows water to move as continuous column continuous column upward through stems of upward through stems of plantsplants

Water Is a Good SolventWater Is a Good Solvent

Ions and polar molecules dissolve Ions and polar molecules dissolve easily in water easily in water

When solute dissolves, water When solute dissolves, water molecules cluster around its ions or molecules cluster around its ions or molecules and keep them separatedmolecules and keep them separated

Fig. 2.16, p. 29

Na+

Cl–

– –

––

––

–

––

– –

+ ++

+

+

+

+

+

+

+

+

++ +

+

+

+

+

Spheres of Hydration

Affects on WeatherAffects on Weather

Releases heat when condensation occurs.Releases heat when condensation occurs.

Absorbs heat when evaporation occurs. Absorbs heat when evaporation occurs.

Impact:Impact: 1.1. Weather is cooler on the shore than Weather is cooler on the shore than

inland during the summer.inland during the summer.2.2. Weather is warmer on the shore than Weather is warmer on the shore than

inland during the winter. inland during the winter.

DensityDensity

Density of water decrease when it Density of water decrease when it moves from the liquid to the solid moves from the liquid to the solid state.state.

Impact:Impact: Allows for organisms to survive Allows for organisms to survive in colder aquatic environments and in colder aquatic environments and

insulates the water below preventing insulates the water below preventing the seas and lakes from freezing.the seas and lakes from freezing.

BACK TO CHEMISTRY!!!!BACK TO CHEMISTRY!!!!

Mixtures, Solutions and Mixtures, Solutions and SuspensionsSuspensions

A mixture is composed of 2 or more A mixture is composed of 2 or more elements or compounds that are elements or compounds that are physically mixed but not combined.physically mixed but not combined.

Examples: salt and pepper, sand, Examples: salt and pepper, sand, atmosphereatmosphere

SolutionsSolutions

Evenly mixed throughout the Evenly mixed throughout the solution.solution.

Solute vs. SolventSolute vs. Solvent

Solute is dissolved by the solvent.Solute is dissolved by the solvent.

Both are either polar or non polar.Both are either polar or non polar.

SuspensionsSuspensions

Materials do not dissolve but they Materials do not dissolve but they are so small they do not settle.are so small they do not settle.

Example: cloudy river waterExample: cloudy river water

What is Blood?What is Blood?

Solution and a suspensionSolution and a suspension

Solution - dissolved sugars, sodium, Solution - dissolved sugars, sodium, potassium, Oxygen, Carbon Dioxidepotassium, Oxygen, Carbon Dioxide

Suspension - white blood cells, red Suspension - white blood cells, red blood cellsblood cells

Acids, Bases and Acids, Bases and pHpH

Hydrogen Ions: HHydrogen Ions: H++

Unbound protonsUnbound protons

Have important biological Have important biological

effectseffects

Form when water ionizesForm when water ionizes

The pH ScaleThe pH Scale

Measures HMeasures H++ concentration of fluid concentration of fluid Change of 1 on scale means 10X change Change of 1 on scale means 10X change

in Hin H++ concentration concentration

Highest HHighest H+ + Lowest H Lowest H++

0---------------------7-------------------140---------------------7-------------------14

Acidic Neutral BasicAcidic Neutral Basic

Examples of pHExamples of pH

Pure water is neutral with pH of 7.0 Pure water is neutral with pH of 7.0 AcidicAcidic

Stomach acid: pH 1.0 - 3.0Stomach acid: pH 1.0 - 3.0 Lemon juice: pH 2.3Lemon juice: pH 2.3

BasicBasic Seawater: pH 7.8 - 8.3Seawater: pH 7.8 - 8.3 Baking soda: pH 9.0Baking soda: pH 9.0

Fig. 2.17, p. 30

Acids & BasesAcids & Bases

AcidsAcids Donate HDonate H++ when dissolved in water when dissolved in water

Acidic solutions have pH < 7Acidic solutions have pH < 7

BasesBases Accept HAccept H++ when dissolved in water when dissolved in water

Basic solutions have pH > 7Basic solutions have pH > 7

Weak and Strong AcidsWeak and Strong Acids

Weak acidsWeak acids Reluctant HReluctant H++ donors donors Can also accept H after giving it upCan also accept H after giving it up

Carbonic acid (HCarbonic acid (H22COCO33) is example) is example

Strong acidsStrong acids Completely give up HCompletely give up H++ when when

dissolveddissolved Hydrochloric acid (HCl) is exampleHydrochloric acid (HCl) is example

Buffer SystemsBuffer Systems

Minimize shifts in pHMinimize shifts in pH

Partnership between weak acid and Partnership between weak acid and base it forms when dissolvedbase it forms when dissolved

Two work as pair to counter shifts in Two work as pair to counter shifts in pHpH

Carbonic Acid-Carbonic Acid-Bicarbonate Buffer Bicarbonate Buffer

SystemSystem When blood pH rises, carbonic acid When blood pH rises, carbonic acid

dissociates to form bicarbonate and Hdissociates to form bicarbonate and H++

HH22C0C033 -----> HC0 -----> HC033-- + H + H++

When blood pH drops, bicarbonate binds When blood pH drops, bicarbonate binds

HH++ to form carbonic acid to form carbonic acid

HC0HC033-- + H + H++ -----> H -----> H22C0C033

SaltsSalts

Compounds that release ions other than Compounds that release ions other than HH++ and OH and OH-- when dissolved in water when dissolved in water

Example: NaCl releases NaExample: NaCl releases Na++ and Cl and Cl––

Many salts dissolve into ions that play Many salts dissolve into ions that play important biological roles important biological roles

End of Chapter 2End of Chapter 2