Basic Chemistry

Important for understanding the complex molecules that are essential for life

Element: Substance that cannot be broken down to other substances

by chemical reaction Elements are composed of atoms Atom: The smallest unit of matter with the properties of an element Four elements account for 96% of the mass of living organisms
Hydrogen (H), Carbon (C), Nitrogen (N), Oxygen (O)

Atoms composed of 3 types of subatomic particles

Nucleus

Electrons

Nuclear: Proton: Charge: +1; mass ~ 1 dalton Neutron: uncharged; mass ~ 1 dalton In orbit: Electron (e-); charge: -1; mass: negligible;
# of protons = # of electrons in a neutral atom Helium (He)

Proton number defines an element

The atomic number
-Is the number of protons -Is unique to each element -Is written as a subscript

The mass number:

-Is the sum of protons and neutrons in the nucleus of an atom

-Is about the atomic mass of an atom (total mass of the atom)
-Is written as a superscript

Isotopes: different forms of an element

Isotopes of a given element: Differ in the number of neutrons in the nucleus Have the same number of protons
Radioactive isotopes :
Unstable: spontaneously decay into more stable forms, releasing energy/particles Useful in biomedical research but can also cause damage

A compound
A substance consisting of two or more elements in a fixed ratio Has characteristics different from those of its elements

Sodium

Chloride

Sodium Chloride

Were interested in compounds that exist in living organisms

Electron behavior is the basis for how atoms assemble into these compounds

The electrons of an atom

Differ in the amounts of energy they possess

More energy, more distant

Each energy level = electron shell

Valence electrons
Are those in the outermost, or valence shell
Determine the chemical behavior (reactivity) of an atom

Valence electrons
Full shell: not reactive (inert) Shell less than full, atoms can gain, lose, or share e-; are reactive
Hydrogen 1H First shell Helium 2He

Lithium 3Li

Beryllium 4Be

Boron 5B

Carbon 6C

Nitrogen 7N

Oxygen 8O

Fluorine 9F

Neon 10Ne

Second shell

Sodium 11Na

Magnesium 12Mg

Aluminum 13Al

Silicon 14Si

Phosphorus 15P

Sulfur 16S

Chlorine 17Cl

Argon 18Ar

Third shell

Most valence shells have eight electrons Octet rule: 8 electrons in valence shell = Stable atom

Chemical bond:
An attractive force that links two atoms together
Permits atoms to complete their valence shells, through sharing or transfer of electrons

The number of bonds that an atom makes is directly related to how many valence electrons it has
ATOM # of Valence electrons Bonding capacity (valence)

H
C N O

1
4 5 6

1
4 3 2

Covalent bonds involve shared electrons A molecule: 2 or more atoms held together by covalent bonds
Covalent bond: drawn by single line, which depicts 2 e- being shared

H OH H2N C CH2 H

Multiple covalent bonds are possible between some atoms these are drawn out using a single line for every 2 electrons involved

O
Triple bond

Double bond

N C CH

Types and positions of bonds determines 3-dimensional structure of molecules

Covalent bonds
Can be nonpolar the electrons are shared equally by the 2 atoms

H OH H2N C CH2 H

Can form between atoms of the same element (e.g. H2) (Would these be polar or not?) Can form between atoms of different elements

Can be polar the electrons are shared unequally between the 2 atoms

HOH
Electronegativity
The attractive force that an atom exerts on electrons More electronegative, stronger pull on electrons Depends on number protons, distance from electrons

Unequal sharing of electrons in polar covalent bonds

If the covalent bond is polar then each atom will take on a partial charge
The more electronegative atom will adopt a partial negative charge (-) The less electronegative atom will adopt a partial positive charge (+)

O H H2O H

Ionic Bonds
-Result from the transfer of electrons -Form by electrical attraction -In some cases, atoms strip electrons away from their bonding partners
(When great differences in electronegativity; the electron is transferred between atoms) This creates ions: charged atoms with more or fewer electrons than usual

-Attraction between a positively charged ion (cation) and a negatively charged ion (anion) creates an ionic bond

Na

Cl

Na

Cl

Na Sodium atom

Cl Chlorine atom

Na+ Sodium ion (a cation)

Cl
Chloride ion (an anion)

Sodium chloride (NaCl)

Strength of Chemical Bonds

Strong: Covalent bonds (very strong) Ionic bonds in solids

Weak but important to living systems:

-Ionic bonds in water -Hydrogen bonds -Van der Waals interactions

Hydrogen Bonds
A hydrogen bond
Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom
+

Water (H2O)

H O H +
A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.

Ammonia (NH3)

N H + H

H
+

Hydrogen bonds are very important in biology

-Water molecules interact with each other through hydrogen bonds -The form of many proteins is related to specific H-bonds

-These bonds are the essence of the DNA double helix

Van der Waals interactions

Occur when transiently positive and negative regions of nonpolar molecules attract each other
Occur due to transient changes in electron distribution

(There are so many Van der Waals interactions between geckos toe hair tip molecules and wall surface molecules that they enable gecko to climb a wall)

Chemical reactions
-Are the making and breaking of chemical bonds -Convert reactants to products

2 H2 Reactants

O2 Reaction

2 H2O Products

-Are reversible

Chapter 2 Self-quiz questions: 2, 3, 4, 6, 7