Cellular Chemistry

Ch 2

Elements of life– Life primarily

consists of C, H, O, N

– Rest are present in small amounts called trace elements

Table 2.1

Trace Elements

• Essential to life

• Occur in minute amounts

• common additives to food and water

• Deficiencies can cause various physiological conditions

Subatomic ParticlesProtons- positive charge

Found in the nucleus

Neutrons- neutral charge

Protons and neutrons occupy the nucleus

Electrons- negative charge

Arranged in electron shells around the nucleus Figure 2.4A

+

+

– –

+

–

2

2

2

Protons

Neutrons

Electrons

Massnumber = 4

+

+

2e–

Electroncloud

Nucleus

Differences in ElementsDifferences in ElementsAtoms of each element

always have the same number of protons

Atomic Number=# protons

Mass Number (atomic weight) = Protons + neutrons

Atoms have no overall charge, thus…

Figure 2.4B

+

–

6

6

6

Protons

Neutrons

Electrons

Mass # = 12

+ +

6e–

Nucleus

Electroncloud

Thus….Thus….Number of protons (+ charge) must be equal Number of protons (+ charge) must be equal

to the number of electrons (-)to the number of electrons (-)

For any element:For any element:

• Number of Protons = Atomic NumberNumber of Protons = Atomic Number

• Number of Electrons = Number of Number of Electrons = Number of Protons = Atomic NumberProtons = Atomic Number

• Number of Neutrons = Mass Number - Number of Neutrons = Mass Number - Atomic NumberAtomic Number

ExampleExample

KrKr

KryptonKrypton

Atomic # = 36Atomic # = 36

Atomic weight = 84Atomic weight = 84

# Protons=?# Protons=?

# Neutrons=?# Neutrons=?

# Electrons=?# Electrons=?

CompoundsCompoundsChemical elements combine in fixed ratios to

form compounds

Different combinations of atoms determine the unique properties of each compound

Sodium Chlorine Sodium ChlorideFigure 2.3

IsotopesIsotopesThe number of neutrons in an atom may vary The number of neutrons in an atom may vary

• Variant forms of an element are called Variant forms of an element are called isotopes isotopes

• Some isotopes are radioactiveSome isotopes are radioactive

Table 2.4

Radioactive isotopesIsotope having an unstable nucleus

-nucleus decays emitting particles until stable

-Ex: Tritium (hydrogen 3)

strontium 90

phosphorus 32

uranium 238

Biological Connection

• Irradiation– A process of disinfestation, pasteurization or

sterilization of food products.– Bacterial spores and viruses not inactivated

by irradiation– Could still be contaminated by food-service

workers after irradiation

Biological Connection• Research

– Radioactive tracers enable researchers to follow particular molecules as they undergo change such as through photosynthesis

• Medical– Kidney disordersKidney disorders– Medical ImagingMedical Imaging

• PET scansPET scans

PET scan image of Parkinson's diseased brainBrown.edu 2008

Electrons, Electrons, Electrons!Electrons, Electrons, Electrons!

• The active part of the atomThe active part of the atom– Only part directly involved in chemical activityOnly part directly involved in chemical activity

• Interactions between electrons form chemical Interactions between electrons form chemical bondsbonds

• Electron shellsElectron shells– Arranged in shells, which may contain Arranged in shells, which may contain

different numbers of electronsdifferent numbers of electrons– Shells are “Full” with either 2 or 8 electronsShells are “Full” with either 2 or 8 electrons

Electron arrangement determines the chemical properties of an atom

– Electrons in an atom are arranged in shells, which may contain different numbers of electrons

Hydrogen (H)Atomic number = 1

Electron

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Outermost electron shell (can hold 8 electrons)

First electron shell (can hold 2 electrons)

Figure 2.6

Electron Shells

Electron shells• Valence electron shell

– Outermost shell of electrons– These electrons interact with other atoms

Hydrogen (H)Atomic number = 1

Electron

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Outermost electron shell (can hold 8 electrons)

First electron shell (can hold 2 electrons)

Figure 2.6

Electronegativity

• Atom’s attraction for shared electronsAtom’s attraction for shared electrons– Greater the electronegativity, stronger the pull Greater the electronegativity, stronger the pull

on e-on e-

Covalent BondsCovalent Bonds•Pairs of e- shared Pairs of e- shared between pairs of between pairs of atomsatoms

–# of bonds is equal # of bonds is equal to additional e- to additional e- necessary to fill the necessary to fill the outer shellouter shell

•Polar and Non-polarPolar and Non-polar

Covalent bond Diamond with 4 covalent bondsinfo.lu.farmingdale.edu/.../atomicbonds.html

PolarityPolarity

• Non-polar covalent- When the atoms exert Non-polar covalent- When the atoms exert a equal pull on the e-a equal pull on the e-– Overall charge of 0Overall charge of 0

• Polar covalent- when the atoms exert an Polar covalent- when the atoms exert an unequal pull on the e-, bond is unequal pull on the e-, bond is – Overall charge on the more electronegative Overall charge on the more electronegative

atom is partially negative and the less atom is partially negative and the less electronegative atom is partially positiveelectronegative atom is partially positive

Polar moleculesPolar molecules

• Unequal e- sharing Unequal e- sharing produces polar bondsproduces polar bonds

(–) (–)

(+) (+)

O

HH

Figure 2.9 Water Molecule

IonsIons

• Created when an atom gains or looses and electron

• Results in an net positive or negative charge depending on if the atom gained or lost the e-

• Anion has neg chrge• Cation has positive charge

Ionic BondsIonic BondsAttractions between ions of opposite chargeAttractions between ions of opposite charge

– An electrical attraction between ions with opposite charges An electrical attraction between ions with opposite charges results in an ionic bondresults in an ionic bond

Transfer of electron

NaSodium atom

ClChlorine atom Na+

Sodium ionCl–

Chloride ion

Sodium chloride (NaCl)

Na Cl ClNa

+ ––

–

Figure 2.7A

NaClNaCl

• Na has 1 e- in the outer shellNa has 1 e- in the outer shell

• Cl has 7 e- in the outer shellCl has 7 e- in the outer shell

• Na “donates” its e- to Cl, leaving Na with Na “donates” its e- to Cl, leaving Na with only 2 shells and Cl with a full outer shellonly 2 shells and Cl with a full outer shell

NaClNaCl

The atom is now an ionThe atom is now an ion– Recall that an ion is an atom or molecule with Recall that an ion is an atom or molecule with

an electrical charge form either gaining or an electrical charge form either gaining or loosing electronsloosing electrons

Hydrogen BondsHydrogen Bonds

• Partial + charge allows shared attractions with – charged molecules

• + charged region always H

Hydrogen bond(+)

(+)

H

H(+)

(+)

(–)

(–)

(–)(–)

O

Figure 2.10

Water and H bonding

1. H2O is asymmetric

2. Each of the two covalent bonds are highly polarized

3. All three atoms are adept at forming H bonds

The importance of hydrogen bonding• Cohesion between HCohesion between H220 molecules0 molecules

– Droplet formationDroplet formation– TransportationTransportation

• Adhesion to substrateAdhesion to substrate• Surface tensionSurface tension• Temperature moderation (body and climatic)Temperature moderation (body and climatic)

– When heated, most thermal E is consumed in disrupting When heated, most thermal E is consumed in disrupting the bonds rather than contributing to molecular motionthe bonds rather than contributing to molecular motion

• DensityDensity– Ice vs. liquid waterIce vs. liquid water

Visual representation of a moleculeVisual representation of a molecule

Molecules can be represented in many ways

Table 2.8

Solvent

• Water is the solvent of life dissolving any charged or polar substances

• Solution

• Aqueous solution

• Solvent– Dissolving agent

• Solute– Dissolved substance

pH Scale

• Some molecules disassociate and release H+ or OH-

– pH is measure of H+ ions

pH scale

• A compound that donates H+ ions in solution is an acid– Increases the net H+ ions in solution

• A compound that accepts H+ ions in solution is a base– Increases the net OH- ions in solution

Basic solution

Oven cleaner

Acidic solution

Neutral solution

pH scale0

1

2

3

4

5

6

7

8

9

10

11

12

Lemon juice, gastric juice

Grapefruit juice, soft drink

Tomato juice

Human urine

Pure waterHuman blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Incr

easi

ngly

AC

IDIC

(Hig

her

conc

entr

atio

n of

H+)

NEUTRAL[H+]=[OH–]

H+ H+

H+ OH– H+

H+ H+

OH– H+ H+

OH–

OH–

H+ H+OH–

OH– OH–

H+ H+H+

OH–

OH–

OH– OH–

OH–OH– H+

Incr

easi

ngly

BA

SIC

(Low

er c

once

ntra

tion

of H

+)

OH–

H+

14

13

pH Scale

Each unit is 10 fold change in concentration of H+ ions

• Buffers act to minimize Ph changes– React with free H+

of OH ions– Often weak

acid/base

pH Buffers• Maintain pH stability by alternately

donating and accepting ions

CHEMICAL REACTIONSChemical reactions change the composition of matter

reactants products

2 H2O2 2 H2OFigure 2.17A

Videos

• AtomsAtoms• http://www.youtube.com/user/http://www.youtube.com/user/

greatpacificmedia#p/u/48/pV822HfqT44greatpacificmedia#p/u/48/pV822HfqT44• Ionic and Covalent bondingIonic and Covalent bonding

http://www.youtube.com/watch?http://www.youtube.com/watch?v=QqjcCvzWwwwv=QqjcCvzWwww

• http://www.youtube.com/user/http://www.youtube.com/user/greatpacificmedia#p/u/49/UR4eG60jjQQgreatpacificmedia#p/u/49/UR4eG60jjQQ

• Hydrogen Bonding• http://www.youtube.com/watch?

v=lkl5cbfqFRM&feature=related• http://www.youtube.com/watch?v=cgiNk94XyaI