September 4, 2013

Atoms, Molecules and

Chemical Bonds
Reading: Chapter 2
The Diversity of Life
Bacteria Archaea Eukarya

Protista

Fungi Plantae Animalia

 Unifying Themes
Organization of life: The Cell Theory
The continuity of life: the molecular basis of
inheritance
The diversity of life: Evolutionary change
Unity of life: Evolutionary conservation
Structure is related to function
Living systems need energy because they are
not at equilibrium
Cells and other living structures can sense
and respond to their environment
Two organizing forces in biology:
Evolution and energy
Organisms must acquire energy to
grow, reproduce, avoid predation
and disease, and maintain
homeostasis

Evolution selects those individuals

that are most efficient at doing this
Nature and Science of Biology
1. The Science of Life
2. The Nature of Science
How science is done
Theories are tested hypotheses
3. Darwin and Evolution
The two components of evolution are
genetic variation and natural selection
4. Unifying Themes in Biology
Isaac Asimov
(1920-1992)
1920 Born in Russia
1948 Earned a Ph.D. in Biochemistry from
Columbia and joined the faculty of the
Boston University School of Medicine
1950 Published I, Robot (including the three
laws of robotics) adapted for a Will
Smith movie in 2004
1951 Published the Foundation Trilogy
1952 Coauthored Biochemistry and Human Metabolism
1958 Wrote The World of Carbon and The World of
Nitrogen
1976 Published The Bicentennial Man and Other Stories
later adapted for a Robin Williams movie in 1999
 The World of
Carbon Nitrogen

Glucose Glycine
a carbohydrate an amino acid
 What is
an atom?
Hydrogen
Atomic number = 1
Atomic mass = 1

Oxygen
Atomic number = 8
Atomic mass = 16

We are concerned
with electrons
(atomic number)
 The Periodic Table
Elements most commonly found in biological molecules are
H, C, O, N, P, S
Elements most commonly found as ions are Na, Mg, K, Ca,
Cl, Fe, H
Electron shells: K, L, M, N
Electron orbitals:
s (2), p (6), d (10)

Ks 2
Ls Lp 8
Ms Mp 8
Ns Md Np 18
 Atoms
Atoms like to fill electron shells
Electrons like to be paired
Charges tend to be balanced
 Atoms
Atoms like to fill electron shells
Electrons like to be paired
Charges tend to be balanced

Ks 2
Ls Lp 8
Ms Mp 8
Ns Md Np 18
 Atoms
Atoms like to fill electron shells
Electrons like to be paired
Charges tend to be balanced
 Ionic Bonding
Atoms like to fill electron shells
Electrons like to be paired
Charges tend to be balanced
Ionic Bonding

NaCl
 Ionic Bonding

Ionic bonds
are not
important in
biology,
because the
ions come
apart in
water.
 Covalent Bonding
Atoms like to fill electron shells
Electrons like to be paired
Charges tend to be balanced

Methane

Water
Hydrogen Atoms
Atoms like to fill electron shells
Electrons like to be paired
Charges tend to be balanced

Hydrogen ion Hydrogen gas

(proton) (covalent bond)
 Covalent Bonding
Atoms like to fill electron shells
Electrons like to be paired
Charges tend to be balanced

How many bonds will N form?

 Covalent Bonding
Atoms like to fill electron shells
Electrons like to be paired
Charges tend to be balanced

Ammonia Ammonium
 Covalent bonding rules

H (hydrogen) 1 bond
C (carbon) - 4 bonds
O (oxygen) 2 bonds
S (sulfur) 2 bonds
N (nitrogen) 3 bonds (or 4 with + charge)
 Chemical Structures
A line is used to indicate a covalent bond
(a pair of shared electrons)

Methane
The World of Carbon

Glucose
a carbohydrate
The World of Carbon

Sucrose (C12H22O11)
 The World of Carbon

Benzene (C6H6)
C and H atoms are frequently not labeled
C is assumed at corners
H is assumed where bonds are missing
 The World of Nitrogen

Glycine
an amino acid Adenine
a nucleotide base
 Whats wrong with these
structures?
Ethanol Acetic acid
CH3CH2OH CH3COOH

A) Incorrect name
B) Incorrect atoms in chemical formula
C) Violate the bonding rules on the right side
D) Violate the bonding rules on the left side
 Whats wrong with these
structures?
Ethanol Acetic acid
CH3CH2OH CH3COOH
Polarity
Which of these are polar?

A
B

C
D
Which of these are polar?

Ethanol
(polar)
Octane
(nonpolar)

Glucose
(polar)
Benzene
(nonpolar)
 Ionization
Ammonia (weak base)
NH3 + H+ NH4+
 Ionization
Acetic acid (weak acid)
+ H+
 Summary

Kinds of atoms:
H, C, O, N, S, P, Na, Cl, K, Mg, Ca, Fe
Rules of covalent bonding
Understanding chemical structures
Polarity
Ionization: H+, Na+, Cl-, NH4+, CH3COO-
 Friday

Properties of Water/pH

Reading: Chapter 2