CHAPTER 2 THE CHEMICAL CONTEXT OF LIFE. CHEMICAL ELEMENTS AND COMPOUNDS MATTER: ANYTHING THAT HAS MASS AND TAKES UP SPACE ELEMENT: A SUBSTANCE THAT CANNOT.

CHAPTER 2

THE CHEMICAL CONTEXT OF LIFE

CHEMICAL ELEMENTS AND COMPOUNDS

MATTER: ANYTHING THAT HAS MASS AND TAKES UP

SPACEELEMENT: A SUBSTANCE THAT

CANNOT BE BROKEN DOWN TO OTHER SUBSTANCES

BY CHEMICAL REACTIONS.COMPOUND: A SUBSTANCE CONSISTING

OF 2 OR MORE ELEMENTS COMBINED IN A FIXED RATIO.

LIFE REQUIRES 25 ELEMENTS

96%: C, O, H, N4%: P, S, Ca, K, Na, Cl, Mg >0.01%: TRACE ELEMENTS e.g. B, Cr, Co, Cu, I, Fe, Mn, Zn etc.CHNOPS

ATOMS AND MOLECULES: STRUCTURE DETERMINES

BEHAVIORSUBATOMIC PARTICELSNEUTRONS (NO) PROTONS (p+) ELECTRONS (ē)

ATOMIC NUCLEUS CONSISTS OF p+ AND no.Ē ‘S MOVE IN A “CLOUD” AROUND THE NUCLEUS

TO DESCRIBE THE MASS OF AN ATOM THE UNIT AMU (atomic mass unit) IS USED. Another name

for this unit is the DALTON.

ATOMIC NUMBER

ATOMIC NUMBER: # OF p+’s. Identifies the element

Written as a subscript to the left of the element symbol.

8O

MASS NUMBER

# of p+’s plus the # of no’s

Written as a superscript to the left of an element’s symbol

16OThe number of no’s can be determined by

subtracting the atomic number from the mass number.

ATOMIC WEIGHT

Total mass of an atom (measured in Daltons).

Is approximated in the mass number but is an average of all isotopes.

ISOTOPES

Different atomic forms of an element.

Same # of p+’s, different # of no’s.

Radioactive isotopes are unstable as the nucleus spontaneously decays.Can result in the release of , , and

particles/energy.Used in medicine and research as tracers

Uses for Radioactive Isotopes

A PET (positron-emission tomography) Scan radioactive-labeled glucose (or some other

nutrient) is injected into the patient.The unstable isotope emits a particel called

a positron which collides with ē’s made available by chemical rx’s.

this allows detection of “hot spots” in an organ.

Uses cont.

Used to label a base unit or nutrient to follow it’s incorporation into macromolecules (e.g. follow DNA synthesis).

Autoradiography is used to determine localization of above macromolecules.

Used to treat some kinds of cancer.

Radioactive isotopes can be harmful.

High levels of exposure can lead to radiation sickness, birth defects and cancer.Tokaimura nuclear accidentShiprock Uranium MineChernobyl Nuclear accident

The Energy Levels of Electrons

Atoms are mostly empty space

Only ē’s are directly involved in chemical reactions.

Electrons vary in the amount of energy they possess.Energy: ability to do work

Potential energy: energy of positionKinetic energy: energy of motion

Electrons cont.Matter has a tendency to move to the lowest possible state of potential energy (entropy).

Because of their position around the nucleus, ē’s have potential energy (PE).The farther ē’s are from the nucleus the

more potential energy they contain.Changes of an ē’s PE can only occur in

fixed steps and cannot exist in between these fixed steps.

Energy Levels or Electron Shells

Defined as the different states of PE that an ē has in an atom.

The 1st shell is closest to the nucleus and can contain 2 ē’s. Lowest PE.

The 2nd shell has higher PE and can contain up to 8 ē’s.

The 3rd shell has yet more PE and can contain up to 18 ē’s.

Electrons cont.

In order for an ē to move up a shell it must gain energy (photosynthesis).

In order for an ē to move to a lower shell it must lose energy (fluorescence).Energy lost to environment in the form of

heat or light.

Electron Configuration and Chemical Properties

The behavior of the atom is determined by its ē configuration, mostly those ē’s (valence ē’s) in it’s outermost shell (valence shell).

Atoms with the same # of valence ē’s exhibit similar chemical behavior.

Electron Orbitals

The Bohr model vs. the Electron Cloud model.

The 3-D space where an ē is found 90% of the time is called an orbital.Each shell consists of a specific # of

orbitals, each orbital holding 2 ē’s.The 1st shell has 1 orbital (1s).

S orbitals are spherical in shape.The 2nd shell has 4 orbitals (2s, 2p3).

The p orbitals are dumbell in shape and are at rt. angles with one another.

Orbitals (cont.)

The 3rd and higher shells also have s and p orbitals as well as orbitals of more complex shape.

Reactivity arises from unpaired ē’s in 1 or more orbitals on their valence shells.

Atoms Combine Chemically to Form Molecules

Atoms with incomplete valence shells interact with other atoms to complete its valence shell.

Atoms complete their valence shell by forming chemical bonds.2 types of strong bonds:

Covalent bondsIonic bonds

Covalent Bonds

Occurs when two atoms share a pair of valence ē’s (nonmetal with nonmetal).E.g. when 2 H atoms come close enough

for their s orbitals to overlap they share the ē’s and a bond is formed.

Molecule: 2 or more atoms held together by a covalent bond.

FormulasStructural formulas: H - H; O = OEach line represents 1 covalent bond

(2 ē’s)A single line represents a single

covalent bond (2 ē’s).Double lines represent a double

covalent bond (4 ē’s).

Molecular formulas: H2 or O2

Simply represents the # and kinds of atoms in a molecule.

Bonding Capacity

Bonding capacity (BC) is the # of bonds an atoms is capable of forming.Usually equates to the # of unpaired

valence ē’s.E. g. H has 1 unpaired valence ē so has a BC

of 1. O has 2 unpaired valence ē’s so has a BC of 2.

Exceptions: P has 5 valence ē’s so should have 3 unpaired ē’s therefore having a BC of 3. However, P actually has a BC of 5, able to form 3 sb’s and 1 db.

Nonpolar and Polar Covalent Bonds

Nonpolar covalent bond: bond in which the ē’s are shared equally (H2, CH4).

Polar covalent bond: bond in which the ē’s are not shared equally (H2O). The unequal sharing of electrons in

water causes the O molecule to have a partial (-) charge and each H to have a partial (+) charge.

Ionic BondsIonic bonds: 2 atoms are so unequal in their attraction for valence ē’s that the more electronegative atom strips an ē completely away from its partner.The atom losing an ē takes a (+) charge

becoming an ion (cation).The atom gaining an ē takes a (-) charge

becoming an ion (anion).The oppositely charged atoms then are

attracted to each other forming a bond.

Ionic CompoundsCalled salts.

Often found in nature as crystals arranged in a 3-D lattice (crystal lattice).

Ionic compounds are not molecules.

A neutral ionic compound will have equal (+) and (-) charges within that compound.

However, molecules can also be ions (polyatomic ions). E. g. NH4+

Weak Chemical BondsBonding between molecules!

Advantage:Contact can be brief so molecules can

respond to one another and then separate.Chemical brain signalling: give a momentary

signal only.Types of weak bonds

Ionic bonds (in solution)Hydrogen bondsVan der Waals interactions

Hydrogen Bond and Van der Waals

Hydrogen bonds:forms when a H atom covalently bonded to 1 electronegative atom is attracted to another electro negative atom.E. g. H2O and NH3

van der Waals interactions: formed because ē’s are in constant motion and are not always symmetrical in distribution.

Hydrogen and van der Waals (cont.)

Van der Waals can form betweenDifferent regions of a single large

molecule.Between regions of different molecules.

Individually they are weak bonds but have a cummulative effect and are used to reinforce 3-D shapes of molecules.

Molecule’s Shape is Related to it’s Function.

Each molecule has a characteristic size and shape.

Shapes can be simple (linear) or complex (tetrahedron, ball and stick).

Molecular shape determines how biological molecules recognize and respond to one another (lock and key).Enzymes, hormones, antibodies

Form and Function (cont.)

Molecular mimic: molecule that mimics an organism’s own molecule to either stimulate a response or gain access to a cell.E. g. Morphine alters pain perception

by mimicing endorphins. Some pathogens gain access to cells by mimicing the binding sites of some hormones.

Chemical Reactions Make and Break Chemical Bonds.

Chemical Rx: the making and breaking to chemical bonds leading to changes in the composition of matter.A chemical rx rearranges atoms to form

new compounds with new characteristics. Indications a chemical rx has occurred.

Gas production Precipitate formation energy change (temperature or light) color change

Chemical vs Physical Changes

Chemical changes are not reversable.

Physical changes do not change the composition of the matter and are reversible. Examples

Phase changesColor changes due to change in pH. Increases in surface area

Parts of a Chemical Rx.

2H2 + O2 2H2O

Reactants: H2 and O2Product: H2OCoefficient: 2H2 (# of molecules)

Subscript: 2H2 (# of atoms)

Chemical rx (cont.)

Chemical equilibriumAs products accumulate, collisions result in

a reverse reaction.The point at which the forward and

backward reactions offset one another exactly is called chemical equilibrium.

Denoted by