The Chemistry of LifeThe Chemistry of Life

Chapter 3Chapter 3

AtomsAtoms

Organisms are chemical machinesOrganisms are chemical machines– one must know chemistry in order to understand one must know chemistry in order to understand

biologybiology Any substance in the universe that has Any substance in the universe that has

mass and occupies space is comprised of mass and occupies space is comprised of mattermatter

MATTERMATTER– Anything that takes up space and has massAnything that takes up space and has mass– Can exist as a liquid, solid, or gas Can exist as a liquid, solid, or gas – All matter is made up of All matter is made up of atomsatoms

AtomsAtoms

AtomAtom = smallest particle a substance can be = smallest particle a substance can be divided into that can retain its propertiesdivided into that can retain its properties

All atoms have the same structureAll atoms have the same structure– at the core is a dense nucleus comprised of two at the core is a dense nucleus comprised of two

types of subatomic particlestypes of subatomic particles protonsprotons (positively charged) (positively charged) neutronsneutrons (no associated charge) (no associated charge)

– orbiting the nucleus is a cloud of another orbiting the nucleus is a cloud of another subatomic particlessubatomic particles electronselectrons (negatively charged) (negatively charged)

AtomsAtoms An atom can be characterized by: An atom can be characterized by:

– Atomic NumberAtomic Number the number of protons in the nucleusthe number of protons in the nucleus atoms with the same atomic number exhibit the same atoms with the same atomic number exhibit the same

chemical properties and are considered to belong to the chemical properties and are considered to belong to the same same elementelement

e.g. Carbon = C: atomic number = 6e.g. Carbon = C: atomic number = 6

– Atomic Mass (mass number) Atomic Mass (mass number) the number of protons plus neutrons in the nucleusthe number of protons plus neutrons in the nucleus electrons have negligible mass (1/1840 dalton)electrons have negligible mass (1/1840 dalton) e.g. C: atomic mass = 12.011e.g. C: atomic mass = 12.011

Atomic Number andAtomic Number and MassMass

Note: Hydrogen is unique in that it has 1 proton, but 0 neutrons!

Atomic SymbolAtomic Symbol

Atomic Mass = Number of Protons +Atomic Mass = Number of Protons + Number of NeutronsNumber of Neutrons

Atomic Number = The Number of ProtonsAtomic Number = The Number of Protons in the Nucleus in the Nucleus

AtomsAtoms

Electrons determine the chemical behavior Electrons determine the chemical behavior of atomsof atoms– These subatomic components are the parts of These subatomic components are the parts of

the atom that come close enough to each other the atom that come close enough to each other in nature to interactin nature to interact Same charges repel each otherSame charges repel each other Opposite charges attract each otherOpposite charges attract each other Electrons can be sharedElectrons can be shared

AtomsAtoms

Electrons are associated with energyElectrons are associated with energy– Potential energy: Potential energy: energy of positionenergy of position

e.g. Rollercoaster at top of peake.g. Rollercoaster at top of peak e.g. As electrons move away from core, they e.g. As electrons move away from core, they

increase potential energyincrease potential energy

– The field of energy around an atom is arranged The field of energy around an atom is arranged as levels called as levels called electron shellselectron shells

– OrbitalsOrbitals are the location electrons are most are the location electrons are most likely to be found within this volume of spacelikely to be found within this volume of space

Electron Arrangement of Atoms

1 electron 6 electrons 7 electrons 8 electrons

AtomsAtoms

Electron shells have specific numbers of Electron shells have specific numbers of orbitals that may be filled with electronsorbitals that may be filled with electrons– atoms that haveatoms that have incomplete incomplete electron orbitals electron orbitals

tend to be more reactivetend to be more reactive– atoms will lose, gain, or share electrons in order atoms will lose, gain, or share electrons in order

to fill completely their outermost electron shellto fill completely their outermost electron shell– these actions are the basis of chemical bondingthese actions are the basis of chemical bonding

How many electron shells?How many electron shells? How many electrons in first How many electrons in first

shell?shell? How many electrons in How many electrons in

second shell?second shell? How many electrons in How many electrons in

third shell?third shell? How many total electrons?How many total electrons? What is Atomic Number?What is Atomic Number? What is Atomic Mass?What is Atomic Mass?

AtomsAtoms

Sodium atom = Na

ElementsElements Basic building block of Basic building block of

mattermatter 92 naturally occurring 92 naturally occurring

elementselements Only Only 66 elements make up elements make up

most of the body weight of most of the body weight of organisms organisms – C C CarbonCarbon– H H HydrogenHydrogen– N N NitrogenNitrogen– O O OxygenOxygen– P P Phosphorus Phosphorus– S S Sulfur Sulfur

IonsIons IonsIons – atoms that have gained or lost one or – atoms that have gained or lost one or

more electronsmore electrons– Gaining an electron makes gives a negative Gaining an electron makes gives a negative

chargecharge– Losing an electron gives a positive chargeLosing an electron gives a positive charge

For Example:For Example:– Sodium ion has 11 protons, 10 electronsSodium ion has 11 protons, 10 electrons– Does this sodium ion have a positive or negative Does this sodium ion have a positive or negative

charge?charge?– A negative ion could also form if an extra electron A negative ion could also form if an extra electron

were addedwere added

Sodium Ion Sodium Ion

IsotopesIsotopes

Isotopes Isotopes – atoms that have the same number of – atoms that have the same number of protons but different numbers of neutronsprotons but different numbers of neutrons– most elements in nature exist as mixtures of different most elements in nature exist as mixtures of different

isotopesisotopes C-12: 6 protons, 6 neutrons, 6 electronsC-12: 6 protons, 6 neutrons, 6 electrons C-14: 6 protons, 8 neutrons, 6 electronsC-14: 6 protons, 8 neutrons, 6 electrons

Some isotopes are unstable and break up into Some isotopes are unstable and break up into particles with lower atomic numbersparticles with lower atomic numbers– this process is known as this process is known as radioactive decayradioactive decay– Radioactive isotopes can be used in nuclear medicineRadioactive isotopes can be used in nuclear medicine

and for dating fossilsand for dating fossils

FigureFigure 3.5 Isotopes of the element carbon3.5 Isotopes of the element carbon

MoleculesMolecules A A moleculemolecule is a group of atoms held together by energy is a group of atoms held together by energy

– e.g. water (He.g. water (H22O), sodium chloride (NaCl), oxygen (OO), sodium chloride (NaCl), oxygen (O22))– The energy holding two atoms together is called a The energy holding two atoms together is called a chemical bondchemical bond

Atoms can interact in 3 ways:Atoms can interact in 3 ways:– 1. Share one or more electrons1. Share one or more electrons– 2. Accept extra electrons2. Accept extra electrons– 3. Donate electrons to another atom3. Donate electrons to another atom

There are 3 principal types of chemical bondsThere are 3 principal types of chemical bonds1.1. IonicIonic2.2. CovalentCovalent3.3. HydrogenHydrogen

IONIC BONDSIONIC BONDS

Ionic bondsIonic bonds involve the involve the attraction of opposite attraction of opposite electrical chargeselectrical charges

• Transfer of electrons from one atom to another

Molecules comprised of Molecules comprised of these bonds are often these bonds are often most stable as most stable as crystalscrystals

Remember:Remember: – An An IONION is an atom that with is an atom that with

a chargea charge

Fig. 3.8(a)The formation of the ionic bond in table salt

COVALENT BONDSCOVALENT BONDS

– – Covalent bondsCovalent bonds form between two atoms form between two atoms when they when they shareshare electrons electrons– The number of electrons shared varies The number of electrons shared varies

depending on how many the atom needs to fill depending on how many the atom needs to fill its outermost electron shellits outermost electron shell

– Covalent bonds are strongerCovalent bonds are stronger than ionic bonds than ionic bonds

COVALENT BONDINGCOVALENT BONDING

A A covalentcovalent bond bond– Each Hydrogen has 1 Each Hydrogen has 1

electron in shellelectron in shell– Sharing 2 electrons fills the Sharing 2 electrons fills the

shell, increasing stabilityshell, increasing stability

A A double covalentdouble covalent bond bond– Sharing 2 pairs of electronsSharing 2 pairs of electrons– Oxygen has total of 8 Oxygen has total of 8

electrons (2 in inner shell, 6 electrons (2 in inner shell, 6 in outer shell)in outer shell)

– Sharing 2 more fills its outer Sharing 2 more fills its outer shell, increasing stabilityshell, increasing stability

HYDROGEN BONDSHYDROGEN BONDS

Hydrogen bondsHydrogen bonds form from covalent bonds form from covalent bonds created by an atom’s created by an atom’s electronegativityelectronegativity– CreateCreate partial charges in atoms that are partial charges in atoms that are

unequally sharing electronsunequally sharing electrons– Are weak bondsAre weak bonds

Electronegativity Electronegativity is the tendency of one is the tendency of one atom’s nucleus to better attract the shared atom’s nucleus to better attract the shared electrons from another nucleuselectrons from another nucleus

Hydrogen bonding of Water Hydrogen bonding of Water MoleculesMolecules

Water molecules contain two covalent bondsWater molecules contain two covalent bonds

HYDROGEN BONDSHYDROGEN BONDS

Hydrogen bondsHydrogen bonds form in association with form in association with polar moleculespolar molecules– each atom with a partial charge acts like a magnet to bond weakly each atom with a partial charge acts like a magnet to bond weakly

to another polar atom with an opposite chargeto another polar atom with an opposite charge– the additive effects of many hydrogen bonding interactions can add the additive effects of many hydrogen bonding interactions can add

collective strength to the bondscollective strength to the bonds

Figure 3.10 Hydrogen bonding water molecules

Hydrogen Bonds Give Water Unique Hydrogen Bonds Give Water Unique PropertiesProperties

Water is essential for lifeWater is essential for life– The chemistry of life is water chemistry!The chemistry of life is water chemistry!

Water is a polar moleculeWater is a polar molecule– The partial charges of hydrogen bonds creates The partial charges of hydrogen bonds creates

polaritypolarity– Water can form hydrogen bondsWater can form hydrogen bonds– Hydrogen bonding confers on water many Hydrogen bonding confers on water many

different special propertiesdifferent special properties

Hydrogen Bonds Give Water Unique Hydrogen Bonds Give Water Unique PropertiesProperties

Heat StorageHeat Storage– Water temperature changes slowly and holds temperature wellWater temperature changes slowly and holds temperature well

This is due to the large number of H bonds many water molecules will This is due to the large number of H bonds many water molecules will form with each other, it takes a lot of energy to break them (and raise form with each other, it takes a lot of energy to break them (and raise temperature)temperature)

Ice FormationIce Formation– Few hydrogen bonds break at low temperaturesFew hydrogen bonds break at low temperatures

Water becomes less dense as it freezes because hydrogen bonds Water becomes less dense as it freezes because hydrogen bonds stabilize and hold water molecules farther apartstabilize and hold water molecules farther apart

High Heat of VaporizationHigh Heat of Vaporization– At high temperatures, hydrogen bonds can be brokenAt high temperatures, hydrogen bonds can be broken

water requires tremendous energy to vaporize because of all the water requires tremendous energy to vaporize because of all the hydrogen bonds that must be brokenhydrogen bonds that must be broken

Hydrogen Bonds Give Water Unique Hydrogen Bonds Give Water Unique PropertiesProperties

Water molecules are stickyWater molecules are sticky– CohesionCohesion – when one polar – when one polar

water molecule is attracted water molecule is attracted to another polar water to another polar water moleculemolecule

– AdhesionAdhesion – when OTHER – when OTHER polar molecules water are polar molecules water are attracted to a water moleculeattracted to a water molecule

Figure 3.12

Hydrogen Bonds Give Water Unique Hydrogen Bonds Give Water Unique PropertiesProperties

Water is highly polarWater is highly polar– in solution, water molecules tend to form the in solution, water molecules tend to form the

maximum number of hydrogen bondsmaximum number of hydrogen bonds HydrophilicHydrophilic moleculesmolecules are attracted to water and are attracted to water and

dissolve easily in itdissolve easily in it– these molecules are also polar and can form hydrogen these molecules are also polar and can form hydrogen

bondsbonds

Hydrophobic Hydrophobic moleculesmolecules are repelled by water and are repelled by water and do not dissolvedo not dissolve

– these molecules are non-polar and do not form hydrogen these molecules are non-polar and do not form hydrogen bondsbonds

Acids and BasesAcids and Bases

When water ionizes, it releases an equal number When water ionizes, it releases an equal number of hydrogen ions (Hof hydrogen ions (H++) and hydroxide ions (OH) and hydroxide ions (OH--).).

Water IonizesWater Ionizes

The amount of ionized hydrogen from water in a The amount of ionized hydrogen from water in a solution can be measured as pHsolution can be measured as pH

The pH scale is The pH scale is logarithmiclogarithmic, which means that a pH , which means that a pH scale difference of 1 unit actually represents a 10-fold scale difference of 1 unit actually represents a 10-fold change in hydrogen ion concentrationchange in hydrogen ion concentration– e.g. pH of 4 has 10x greater H+ concentration than pH of 5e.g. pH of 4 has 10x greater H+ concentration than pH of 5– e.g. pH of 4 has 100x greater H+ concentration than pH of 6e.g. pH of 4 has 100x greater H+ concentration than pH of 6

pH difference of 2; 10 x 10 = 100 pH difference of 2; 10 x 10 = 100

pH = -log[H+]

The pH scaleThe pH scale

Water IonizesWater Ionizes Pure water has a pH of 7Pure water has a pH of 7

– there are equal amounts of [H+] relative there are equal amounts of [H+] relative to [OH-]to [OH-]

AcidAcid – any substance that – any substance that dissociates in water and increases dissociates in water and increases the [Hthe [H++]]– acidic solutions have pH values below 7acidic solutions have pH values below 7

Base Base – any substance that combines – any substance that combines with [Hwith [H++] when dissolved in water] when dissolved in water– basic solutions have pH values above 7basic solutions have pH values above 7

Water IonizesWater Ionizes

The pH in most living cells and their environments The pH in most living cells and their environments is fairly close to 7is fairly close to 7– proteins involved in metabolism are sensitive to any pH proteins involved in metabolism are sensitive to any pH

changeschanges

Acids and bases are routinely encountered by Acids and bases are routinely encountered by living organismsliving organisms– from metabolic activities (i.e., chemical reactions)from metabolic activities (i.e., chemical reactions)– from dietary intake and processingfrom dietary intake and processing

Organisms use Organisms use buffersbuffers to minimize pH to minimize pH disturbancesdisturbances

Water IonizesWater Ionizes

BufferBuffer – a chemical substance that takes up – a chemical substance that takes up or releases hydrogen ionsor releases hydrogen ions

– Buffers don’t remove the acid or the base Buffers don’t remove the acid or the base affecting pH, but minimize their effect on itaffecting pH, but minimize their effect on it

– Most buffers are pairs of substances, one an Most buffers are pairs of substances, one an acid and one a baseacid and one a base

Buffer ExampleBuffer Example

Carbonic acid and bicarbonate in human bloodCarbonic acid and bicarbonate in human blood Interact in a pair of reversible reactions Interact in a pair of reversible reactions

– COCO2 2 + H+ H22O O H H22COCO33

– HH22COCO33 H H++ + HCO + HCO33-

If H+ is added, HCO3- can pick up H+ added to

form H2CO3

If H+ is removed, it disassociates to release more H+ into blood