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Transcript of 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
http://www.bozemanscience.com/biology-main-page/
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