Chapter 2Chapter 2

Chemical Foundations for Chemical Foundations for CellsCells

Chapter OutlineChapter Outline

Review of elements and atomic structureReview of elements and atomic structure Radioactive elements and health/medicine Radioactive elements and health/medicine

Chemical bondingChemical bonding IonicIonic Covalent: nonpolar and polarCovalent: nonpolar and polar Hydrogen “bonding”Hydrogen “bonding”

Properties of waterProperties of water Acids, bases, and buffersAcids, bases, and buffers Chemical changeChemical change

Elements Elements (2.1, (2.1, 2.32.3))

Living organisms are composed of matterLiving organisms are composed of matter Matter is composed of Matter is composed of elementselements

• Element - substance that cannot be broken down Element - substance that cannot be broken down into other substances by chemical meansinto other substances by chemical means

Elements are made up of Elements are made up of atomsatoms.. Atoms join together to make Atoms join together to make compoundscompounds..

AtomsAtoms

CompoundsCompounds

Elements Elements (2.1)(2.1)

92 naturally occurring elements 92 naturally occurring elements Life requires ~25 of theseLife requires ~25 of these ~96% of human body is made up of:~96% of human body is made up of:

• Carbon (C)Carbon (C)• Hydrogen (H)Hydrogen (H)• Oxygen (O)Oxygen (O)• Nitrogen (N)Nitrogen (N)

Compounds Compounds (2.1)(2.1)

Atoms of one element can join with Atoms of one element can join with atoms of other elements to form atoms of other elements to form compounds. compounds.

• A given compound is always made of the A given compound is always made of the same elements combined in the same ways.same elements combined in the same ways.

• NaCl – table saltNaCl – table salt

• HH22O - waterO - water

• CC66HH1212OO6 6 - glucose- glucose

Compounds of LifeCompounds of Life

OnlyOnly living organisms have the ability to living organisms have the ability to make the compounds of life:make the compounds of life: Carbohydrates: C, H, OCarbohydrates: C, H, O Lipids: C, H, OLipids: C, H, O Proteins: C, H, O, N, SProteins: C, H, O, N, S Nucleic acids: C, H, O, N, PNucleic acids: C, H, O, N, P

Atoms Atoms (2.3)(2.3)

An atom is the smallest unit of an elementAn atom is the smallest unit of an element Atoms are composed of 3 subatomic Atoms are composed of 3 subatomic

particles: particles: ProtonsProtons NeutronsNeutrons ElectronsElectrons

Subatomic ParticlesSubatomic Particles

Subatomic Subatomic ParticleParticle

ChargeCharge Mass, amuMass, amu Location in Location in atomatom

Electron Electron

(e(e--))

-1-1 0 amu0 amu Outside of Outside of nucleusnucleus

Proton (p)Proton (p) +1+1 ~1 amu~1 amu NucleusNucleus

Neutron (n)Neutron (n) 00 ~1 amu~1 amu NucleusNucleus

Subatomic Particles and the Subatomic Particles and the Elements Elements

Each element has a unique number of Each element has a unique number of protons.protons. Atomic number Atomic number - number of protons in an - number of protons in an

atomatom• Elements are arranged by atomic number on the Elements are arranged by atomic number on the

periodic table.periodic table. Atoms are neutral, therefore # p = # eAtoms are neutral, therefore # p = # e

Number of neutrons is NOT on the Number of neutrons is NOT on the periodic table for most elements….periodic table for most elements…. IsotopesIsotopes - atoms of a given element that differ - atoms of a given element that differ

in the number of neutrons in the nucleusin the number of neutrons in the nucleus• Mass number Mass number – sum of the protons and neutrons in – sum of the protons and neutrons in

an atoms’ nucleusan atoms’ nucleus• The periodic table shows the average of the mass The periodic table shows the average of the mass

numbers for the isotopes of an element.numbers for the isotopes of an element.

Isotopes

Describing IsotopesDescribing Isotopes

Mass number Mass number 1212CCIsotopes of carbonIsotopes of carbon

1212C C carbon-12carbon-12 __ neutrons__ neutrons 1313CC carbon-13carbon-13 __ neutrons__ neutrons 1414CC carbon-14carbon-14 __ neutrons__ neutrons

• All contain ____ protons and electrons.All contain ____ protons and electrons.

Carbon on theCarbon on the

Periodic tablePeriodic table

Isotopes and Radioactivity (RA)Isotopes and Radioactivity (RA)

RA isotope has an unstable nucleus RA isotope has an unstable nucleus Nucleus emits energy and particles in an Nucleus emits energy and particles in an

effort to become more stableeffort to become more stable May change the number of protons in the May change the number of protons in the

nucleus and become a different element.nucleus and become a different element.

Radioactive IsotopesRadioactive Isotopes

Possible to target the energy and detect Possible to target the energy and detect the radioactivity.the radioactivity.

RA isotopes are used:RA isotopes are used: in research to track/follow moleculesin research to track/follow molecules in medicine to treat cancer and diagnose in medicine to treat cancer and diagnose

diseasedisease• Radiation therapy – treatment of localized cancerRadiation therapy – treatment of localized cancer• PET - diagnosis - diagnosis

Radioactive IsotopesRadioactive Isotopes

Overexposure to RA isotopes is Overexposure to RA isotopes is HARMFUL.HARMFUL. Energy emitted damages cells.Energy emitted damages cells.

• radiation therapy takes advantage of this, goal is to radiation therapy takes advantage of this, goal is to damage and kill cancer cellsdamage and kill cancer cells

Exposure to RA can also cause mutations Exposure to RA can also cause mutations that lead to cancersthat lead to cancers• Eg – exposure to RA element radon is the 2Eg – exposure to RA element radon is the 2ndnd

leading cause of lung cancerleading cause of lung cancer

Diagnosis - PET ScansDiagnosis - PET Scans

A radioactive tracer is put into the body. A radioactive tracer is put into the body. Often RA glucoseOften RA glucose

The RA glucose goes to the parts of the The RA glucose goes to the parts of the body that use glucose for energy. body that use glucose for energy. Cancers use glucose differently from normal Cancers use glucose differently from normal

tissue tissue As the radiotracer is broken down positrons As the radiotracer is broken down positrons

are made. This energy appears as a 3-are made. This energy appears as a 3-dimensional image on a computer monitor. dimensional image on a computer monitor.

Electron Arrangement Electron Arrangement (2.5)(2.5)

When compounds form, the electrons of When compounds form, the electrons of the bonding atoms interact in attempt to the bonding atoms interact in attempt to obtain a more stable state.obtain a more stable state.

Some electron arrangements are more Some electron arrangements are more stable than others…….see boardstable than others…….see board

Chemical Bonding Chemical Bonding (2.6-2.7)(2.6-2.7)

Chemical bondingChemical bonding – atoms gain, – atoms gain, lose, or share electron(s) to obtain a lose, or share electron(s) to obtain a stable number of electronsstable number of electrons Can be ionic bond or covalent bondCan be ionic bond or covalent bond

Chemical Bonding - IonicChemical Bonding - Ionic

Ionic Bond – strong attractive force Ionic Bond – strong attractive force between oppositely charged ionsbetween oppositely charged ions Atoms form ions by losing or gaining enough Atoms form ions by losing or gaining enough

electron(s) to obtain a stable # of electrons in electron(s) to obtain a stable # of electrons in their outer shelltheir outer shell

SODIUMATOM11 p+

11 e-

electron transfer

CHLORINEATOM17 p+

17 e-

SODIUMION

11 p+

10 e-

CHLORINEION

17 p+

18 e-

Ionic Bonding

Chemical Bonding - CovalentChemical Bonding - Covalent

Covalent BondCovalent Bond – bonded atoms – bonded atoms shareshare pair(s) of electrons and form pair(s) of electrons and form moleculesmolecules.. Occurs between nonmetals such as: Occurs between nonmetals such as:

C, O, H, N, P, SC, O, H, N, P, S Covalent bonding occurs inCovalent bonding occurs in

• HH22

• OO22

• HH22OO

Two Classes of Covalent BondsTwo Classes of Covalent Bonds

Nonpolar Covalent BondNonpolar Covalent Bond – bonded atoms – bonded atoms share electrons equallyshare electrons equally Occurs between like atoms or between atoms Occurs between like atoms or between atoms

with a similar ability to attract shared electronswith a similar ability to attract shared electrons

Polar Covalent BondPolar Covalent Bond – unequal sharing of – unequal sharing of electrons by the bonded atomselectrons by the bonded atoms Occurs between atoms with very different Occurs between atoms with very different

ability to attract shared electrons ability to attract shared electrons

molecular hydrogen (H2)H—H

Two hydrogen atoms, each with one proton, share two electrons in a single nonpolar covalent bond.

Fig. 2-8b(1), p.25

water (H2O)H—O—H

molecular oxygen (O2)O=O

Two oxygen atoms share four electrons in a nonpolar doublecovalent bond.

Types of Covalent BondsTypes of Covalent Bonds

Nonpolar covalent Nonpolar covalent – bonded atoms – bonded atoms share the electrons equallyshare the electrons equally Examples of nonpolar bonds: Examples of nonpolar bonds:

• HH22

Atoms with different electronegativity Atoms with different electronegativity values form values form polar covalent bondspolar covalent bonds..

• Electronegativity (EN) – measure of an Electronegativity (EN) – measure of an atom’s ability to attract shared electrons in atom’s ability to attract shared electrons in a covalent bonda covalent bond

• Oxygen and nitrogen have fairly large EN Oxygen and nitrogen have fairly large EN values – often values – often - -

• Carbon and hydrogen have low EN values Carbon and hydrogen have low EN values – often – often + +

Polar Covalent – unequal pull on shared Polar Covalent – unequal pull on shared electrons by the bonded atoms electrons by the bonded atoms Results in partial charges on the bonded Results in partial charges on the bonded

atomsatoms

H H

O

+ +

-

Common Polar Covalent BondsCommon Polar Covalent Bonds

O-H N-HO-H N-H

C-O C-O C=OC=O

Label the polarity in each bond.Label the polarity in each bond.

Forces between MoleculesForces between Molecules

Molecules are weakly attracted to each Molecules are weakly attracted to each other by intermolecular (IM) forces,other by intermolecular (IM) forces,

The most important IM force in biology is The most important IM force in biology is the hydrogen “bond” the hydrogen “bond” (2.8)(2.8) Attractive force between Attractive force between + H and – O, N

or F

Hydrogen “bond” is a weak attractive Hydrogen “bond” is a weak attractive force between a force between a + hydrogen and a + hydrogen and a --O, N, or F in a second polar bond O, N, or F in a second polar bond

Water is a polar molecule capable of hydrogen bonding.

Properties of WaterProperties of Water1.1. Water is Water is cohesive and has high surface cohesive and has high surface

tensiontension..

• Cohesion – ability of molecules to Cohesion – ability of molecules to stick togetherstick together

• Surface tension - ability to resist Surface tension - ability to resist rupturing when under tensionrupturing when under tension

Properties of WaterProperties of Water

2)2) Water resists changes in Water resists changes in temperature.temperature.• When heat is applied to an aqueous When heat is applied to an aqueous

solution much of the heat (energy) is used solution much of the heat (energy) is used to break hydrogen bonds, not to increase to break hydrogen bonds, not to increase the movement of the molecules.the movement of the molecules.

Properties of WaterProperties of Water

3)3) Solid water (ice) is less dense than Solid water (ice) is less dense than liquid waterliquid water

• Ice floatsIce floats• Therefore, ice forms on the top of lakes Therefore, ice forms on the top of lakes

and insulates the liquid water below.and insulates the liquid water below.

4)4) Water is a good solvent for ionic Water is a good solvent for ionic compounds and small polar compounds and small polar molecules.molecules.

Water H bonds to polarWater H bonds to polarmolecules like ethanolmolecules like ethanol

Water as solventWater as solvent

Water pulls ions apart and hydrates themWater pulls ions apart and hydrates them

Related TermsRelated Terms

HydrophilicHydrophilic• Water lovingWater loving• Capable of hydrogen bonding to water Capable of hydrogen bonding to water

(polar)(polar)

HydrophobicHydrophobic• Water “fearing”Water “fearing”• Cannot hydrogen bond to water Cannot hydrogen bond to water

(nonpolar)(nonpolar)

Acids, Base, and Buffers Acids, Base, and Buffers (2.14)(2.14)

Many ions are dissolved in the fluids Many ions are dissolved in the fluids in/outside of cells – in/outside of cells – called electrolytescalled electrolytes NaNa++, Ca, Ca+2+2, K, K++

HH++ Level of each ion is criticalLevel of each ion is critical

Our focus is on HOur focus is on H++ (hydrogen ions) (hydrogen ions)

Acids, Base, and BuffersAcids, Base, and Buffers

Acid: Substance that produces HAcid: Substance that produces H++ when when dissolved in water……….dissolved in water………. Examples:Examples:

• Hydrochloric acid – stomach acidHydrochloric acid – stomach acid• Lactic acid – made when cells run out of oxygenLactic acid – made when cells run out of oxygen• Amino acids – building blocks of proteinsAmino acids – building blocks of proteins

Acids, Base, and BuffersAcids, Base, and Buffers

Base: substance that accepts HBase: substance that accepts H+1+1 (hydrogen ions) in water(hydrogen ions) in water Examples:Examples:

• Sodium hydroxide - NaOHSodium hydroxide - NaOH

• Most nitrogen containing compoundsMost nitrogen containing compounds Ammonia – NHAmmonia – NH33

Urea – in urineUrea – in urine Amino acids – building blocks for proteinsAmino acids – building blocks for proteins

Acids, Base, and BuffersAcids, Base, and Buffers

Classify substances as acid, base or Classify substances as acid, base or neutral by their pHneutral by their pH Acids: pH < 7Acids: pH < 7 Base: pH > 7Base: pH > 7 Neutral: pH = 7Neutral: pH = 7

• Pure water has a pH of 7Pure water has a pH of 7

• See page 28See page 28

Acids, Base, and BuffersAcids, Base, and Buffers

How the pH scale worksHow the pH scale works The lower the pH the more acidicThe lower the pH the more acidic The higher the pH the more basic (alkaline)The higher the pH the more basic (alkaline)

A difference of 1 pH unit is a 10-fold A difference of 1 pH unit is a 10-fold difference in acidity or alkalinitydifference in acidity or alkalinity

Why is pH important?Why is pH important?

Most cells require a pH near 7. Most cells require a pH near 7. Above or below this pH for too long and Above or below this pH for too long and

they die.they die.

Proteins function only at specific pHs.Proteins function only at specific pHs.• In lab you will determine the optimal pH for a In lab you will determine the optimal pH for a

protein that is needed to breakdown hydrogen protein that is needed to breakdown hydrogen peroxide in cellsperoxide in cells

Acids, Base, and BuffersAcids, Base, and Buffers

BuffersBuffers: solution that resists changes in : solution that resists changes in pH even when acid or base is addedpH even when acid or base is added Buffers can both produce HBuffers can both produce H++ and neutralize H and neutralize H++ Buffers are key to maintaining pH Buffers are key to maintaining pH

homeostasis homeostasis • Most body solutions are bufferedMost body solutions are buffered

Why is pH important?Why is pH important?

Blood has a pH of 7.3 – 7.4Blood has a pH of 7.3 – 7.4 If the pH is above or below this range for If the pH is above or below this range for

more than a couple of days death occurs.more than a couple of days death occurs. • The blood buffer system helps keep blood pH in a The blood buffer system helps keep blood pH in a

range that supports life.range that supports life.