BIO 2, Lecture 3BIO 2, Lecture 3BIO 2, Lecture 3BIO 2, Lecture 3THE CHEMISTRY OF LIFE I: THE CHEMISTRY OF LIFE I:

ATOMS, MOLECULES, ATOMS, MOLECULES, AND BONDSAND BONDS

–

+

+

H H

O

H2O

• Matter is made up of elements • A substance that cannot be broken

down to other substances by chemical reactions

• 92 naturally-occurring elements (periodic table)

• A compound is a substance consisting of two or more elements in a fixed ratio (e.g. NaCl, MgCl2)• A compound has characteristics

different from those of its elements

Sodium Chloride SodiumChloride

About 25 of the 92 naturally-occurring

elements are essential to living

organisms on Earth

Dwarfing of plants due to nitrogen deficiency

Goiter due to iodine deficiency

• An element’s chemical behavior and properties depend on the structure of its atoms

• Each element consists of unique atoms• An atom is the smallest unit of matter

that still contains the behavior and properties of an element

• Atoms are composed of a nucleus containing protons (+) and (usually) neutrons, and electrons (-) that inhabit defined energy shells around the nucleus

Cloud of negative charge (2 electrons)

Nucleus

Electrons

(b)

(a)

• Atoms of the various elements differ in number of subatomic particles they contain

• An element’s atomic number is the number of protons in its nucleus

• An element’s mass number is the sum of protons plus neutrons in the nucleus

• Atomic mass, the atom’s total mass, can be approximated by the mass number (since electrons are so light)

• All atoms of an element have the same number of protons but may differ in number of neutrons

• Isotopes are two atoms of an element that differ in number of neutrons

• Radioactive isotopes decay spontaneously, giving off particles and energy

Isotopes of hydrogen:

Symbol Name # protons # neutrons Half-life1H Protium 1 0 Stable2H Deuterium 1 1 Stable3H Tritium 1 2 12.3 yrs4H Lab only 1 3 Very

low*5H Lab only 1 4 Very

low*6H Lab only 1 5 Very

low*7H Lab only 1 6 Very

low*

* less than 10-22 seconds

• Some applications of radioactive isotopes in biological research are:

– Dating rocks and fossils– Tracing atoms through metabolic

processes to learn about those processes

– Diagnosing medical disorders

Parent Isotope Stable Daughter

Product Currently Accepted

Half-Life Values

Uranium-238 Lead-206 4.5 billion years

Uranium-235 Lead-207 704 million years

Thorium-232 Lead-208 14.0 billion years

Rubidium-87 Strontium-87 48.8 billion years

Potassium-40 Argon-40 1.25 billion years

Compounds includingradioactive tracer(bright blue)

Human cells

Incubators1 2 3

4 5 6

7 8 950ºC

45ºC

40ºC

25ºC

30ºC

35ºC

15ºC

20ºC

10ºC

Humancells areincubatedwith compounds used tomake DNA. One compound islabeled with 3H.

1

2 The cells areplaced in testtubes; their DNA is isolated; andunused labeledcompounds areremoved.

DNA (old and new)

The test tubes are placed in a scintillation counter.3

Cou

nts

per

min

ute

( 1

,000)

010 2

030

40

50

10

20

30

Temperature (ºC)

Optimumtemperaturefor DNAsynthesis

Cancerousthroattissue

• Energy is the capacity to do work (fight entropy)

• Atoms have mass and therefore have potential energy; E = mc2

• Part of this energy is stored in the nucleus of the atom and part is stored in the energy levels of the electrons• An electron’s state of potential energy is

called its energy level, or electron shell

(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons

Third shell (highest energy level)

Second shell (higher energy level)

Energyabsorbed

First shell (lowest energy level)

Atomicnucleus

(b)

Energylost

• The chemical behavior of an atom is determined by the distribution of electrons in electron shells

• The periodic table of the elements shows the electron distribution for each element

• Valence electrons are those in the outermost shell, or valence shell

• Elements with filled valence shells are inherently stable and don’t readily combine with other elements

Hydrogen

1H

Lithium

3Li

Beryllium

4Be

Boron

5BCarbo

n

6C

Nitrogen

7N

Oxygen

8O

Fluorine

9F

Neon

10Ne

Helium

2He

Atomic number

Element symbolElectron-distributiondiagram

Atomic mass

2He4.0

0Firstshell

Second

shell

Thirdshell

Sodium

11Na

Magnesium

12Mg

Aluminum

13Al

Silicon

14SiPhosphor

us

15P

Sulfur

16SChlorin

e

17Cl

Argon

18Ar

• An orbital is the three-dimensional space where an electron is found 90% of the time

• Each electron shell consists of a specific number of orbitals• 1S (1 orbital; 2 electrons)• 2S (1 orbital; 2 electrons)• 2P (3 different oribitals; 6 electrons)

• The shell is designated by the number, the orbitals by the letter

• Atoms seek filled shells above all else

Electron-distributiondiagram

(a)

(b)

Separate electronorbitals

Neon, with two filled shells (10 electrons)

First shell

Second shell

1s orbital 2s orbital Three 2p orbitals

(c)

Superimposed electronorbitals

1s, 2s, and 2p orbitals

x y

z

•Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms

•These interactions usually result in atoms staying close together, held by attractions called chemical bonds

•A covalent bond is the sharing of a pair of valence electrons by two atoms

•In a covalent bond, the shared electrons count as part of each atom’s valence shell

Hydrogenatoms (2

H)

Hydrogenmolecule (H2)

e- e-

e- e-

e-

e-

Both atoms unstable (unfilled valence shells)

Atoms stable, share electrons

so both have filled valence

shells

• A molecule consists of two or more atoms held together by covalent bonds

• A single covalent bond, or single bond, is the sharing of one pair of valence electrons

• A double covalent bond, or double bond, is the sharing of two pairs of valence electrons

Name andMolecularFormula

Electron-distributio

nDiagram

Lewis DotStructure

andStructural

Formula

Space-fillingModel

(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

(d) Methane (CH4)

COVALENT BONDS

• Covalent bonds can form between atoms of the same element or atoms of different elements

• A compound is a combination of two or more different elements

• Bonding capacity is called the atom’s valence

• Electronegativity is an atom’s attraction for the electrons in a covalent bond

• The more electronegative an atom, the more strongly it pulls shared electrons toward itself

• In a nonpolar covalent bond, the atoms share the electron equally

• In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule (e.g. water)

–

+

+

H H

O

H2

O

The oxygen nucleus has more protons and attracts the shared electrons

more strongly than the hydrogen nuclei

• Rather than sharing electrons, atoms sometimes transfer electrons to their bonding partners because it fills their valence shells (makes them stable)

• An example is the transfer of an electron from sodium to chlorine

• After the transfer of an electron, both atoms have charges• A charged atom (or molecule) is called an

ion• Ions with opposite charges attract to form

ionic bonds

Na

Cl Na

Cl

NaSodium

atomChlorine

atom

Cl Na+Sodium ion

(a cation)

Cl–Chloride

ion(an anion)

Sodium chloride (NaCl)

IONIC BOND

• Compounds formed by ionic bonds are called ionic compounds, or salts

• Salts, such as sodium chloride (table salt), are often found in nature as crystals because they stack easily

Na+

Cl–

• Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules

• Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important

• Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other

• A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

• In living cells, the electronegative partners are usually oxygen or nitrogen atoms

• Hydrogen bonding is important in water, DNA and RNA, proteins, and many other molecules important for life

+

+

+

+

+

Water (H2O)

Ammonia (NH3)

HYDROGEN BOND