Chapter 2 Atoms and Molecules - Unisa Study Notes › wp-content › uploads › 2018 › 12 ›...
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Lecture Presentations by
Nicole Tunbridge and
Kathleen Fitzpatrick
Chapter 2
Atoms and
Molecules
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A Chemical Connection to Biology
Biology is the study of life
Organisms and their environments are subject to
basic laws of physics and chemistry
One example is the use of formic acid by ants to
protect themselves against predators and microbial
parasites
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Figure 2.1
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Figure 2.1a
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Concept 2.1: Matter consists of chemical
elements in pure form and in combinations
called compounds
Organisms are composed of matter
Matter is anything that takes up space and has mass
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Elements and Compounds
Matter is made up of elements
An element is a substance that cannot be broken
down to other substances by chemical reactions
A compound is a substance consisting of two or
more elements in a fixed ratio
A compound has characteristics different from those
of its elements
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Figure 2.2
NaSodium
ClChlorine
NaClSodium chloride
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Figure 2.2a
NaSodium
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Figure 2.2b
ClChlorine
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Figure 2.2c
NaClSodium chloride
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The Elements of Life
About 20–25% of the 92 natural elements are
required for life (essential elements)
Carbon, hydrogen, oxygen, and nitrogen make up
96% of living matter
Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
Trace elements are required by an organism in only
minute quantities
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Table 2.1
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Case Study: Evolution of Tolerance to Toxic
Elements
Some elements can be toxic
Some species can become adapted to environments
containing toxic elements
For example, some plant communities are adapted to
serpentine
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Figure 2.3
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Figure 2.3a
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Figure 2.3b
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Figure 2.3c
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Concept 2.2: An element’s properties depend
on the structure of its atoms
Each element consists of unique atoms
An atom is the smallest unit of matter that still
retains the properties of an element
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Subatomic Particles
Atoms are composed of subatomic particles
Relevant subatomic particles include
Neutrons (no electrical charge)
Protons (positive charge)
Electrons (negative charge)
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Neutrons and protons form the atomic nucleus
Electrons form a “cloud” of negative charge around
the nucleus
Neutron mass and proton mass are almost identical
and are measured in daltons
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Figure 2.4
Cloud of negativecharge (2 electrons)
Nucleus
+
+
Electrons
−
+
+
−
(a) (b)
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Atomic Number and Atomic Mass
Atoms of the various elements differ in number of
subatomic particles
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
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Isotopes
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
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Radioactive Tracers
Radioactive isotopes are often used as diagnostic
tools in medicine
Radioactive tracers can be used to track atoms
through metabolism
They can also be used in combination with
sophisticated imaging instruments
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Figure 2.5
Cancerousthroattissue
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Radiometric Dating
A “parent” isotope decays into its “daughter” isotope
at a fixed rate, expressed as the half-life
In radiometric dating, scientists measure the ratio
of different isotopes and calculate how many half-
lives have passed since the fossil or rock was
formed
Half-life values vary from seconds or days to billions
of years
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The Energy Levels of Electrons
Energy is the capacity to cause change
Potential energy is the energy that matter has
because of its location or structure
The electrons of an atom differ in their amounts of
potential energy
An electron’s state of potential energy is called its
energy level, or electron shell
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Figure 2.6
(a) A ball bouncing down a flightof stairs can come to rest onlyon each step, not between steps.
Third shell (highest energylevel in this model)
Second shell (higherenergy level)
Energyabsorbed
First shell (lowest energylevel)
Energylost
(b)
Atomicnucleus
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Electron Distribution and Chemical Properties
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
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Figure 2.7
Hydrogen
1
First
shell
Atomic mass 4.003
He2 Atomic number
Element symbol
Electrondistributiondiagram
HeliumHe
Lithium
Second
shell
Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon
Sodium
Third
shell
Magnesium Silicon Phosphorus Sulfur Chlorine Argon
2
Li3 Be4 B5 C6 N7 O8 F9 Ne10
Na11 Mg12 AI13 SI14 P15 S16 CI17 Ar18
H
Aluminum
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Figure 2.7a
2 Atomic number
He
4.003
Atomic mass
Element symbol
Electrondistributiondiagram
Helium
2He
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Figure 2.7b
Hydrogen
1
Firstshell
HeliumH 2He
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Figure 2.7c
Lithium
Secondshell
Beryllium Boron Carbon
Sodium
Thirdshell
Magnesium SiliconAluminum
3 4 5 6
11 12 13 14
Li Be B C
Na Mg Al Si
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Figure 2.7d
Secondshell
Thirdshell
Nitrogen Oxygen Fluorine Neon
Phosphorus Sulfur Chlorine Argon
7 8 9 10
15 16 17 18
N O F Ne
P S Cl Ar
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Valence electrons are those in the outermost shell,
or valence shell
The chemical behavior of an atom is mostly
determined by the valence electrons
Elements with a full valence shell are
chemically inert
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Electron Orbitals
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
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Figure 2.8
First shell Second shell
Neon,with twofilled shells(10 electrons)
Firstshell
Secondshell
1s orbital 2s orbital
x
z
Three 2p orbitals
y
(a) Electron distributiondiagram
(b) Separate electron orbitals
1s, 2s, and2p orbitals
(c) Superimposed electron orbitals
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Figure 2.8a
Secondshell
(a) Electron distribution diagram
Neon,with twofilled shells(10 electrons)
Firstshell
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Figure 2.8b
First shell Second shell
x y
1s orbital 2s orbital
z
Three 2p orbitals
(b) Separate electron orbitals
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Figure 2.8c
1s, 2s, and2p orbitals
(c) Superimposed electron orbitals
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Concept 2.3: The formation and function of
molecules depend on chemical bonding
between atoms
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
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Covalent 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
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Figure 2.9_1
Hydrogen atoms (2 H)
+ +
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Figure 2.9_2
Hydrogen atoms (2 H)
+ +
+ +
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Figure 2.9_3
Hydrogen atoms (2 H)
+ +
+ +
+ +
Hydrogenmolecule (H2)
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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
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The notation used to represent atoms and bonding is
called a structural formula
For example, H—H
This can be abbreviated further with a molecular
formula
For example, H2
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Figure 2.10
Name andMolecularFormula
(a) Hydrogen (H2)
ElectronDistribution
Diagram
Lewis DotStructure and
StructuralFormula
Space-FillingModel
H H
(b) Oxygen (O2)
O O
(c) Water (H2O)
O
H
H
(d) Methane (CH4)
H
H
C
H
H
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Figure 2.10a
Name andMolecularFormula
(a) Hydrogen (H2)
Space-FillingModel
ElectronDistribution
Diagram
Lewis DotStructure and
StructuralFormula
H H
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Figure 2.10b
Name andMolecularFormula
Space-FillingModel
ElectronDistribution
Diagram
Lewis DotStructure and
StructuralFormula
(b) Oxygen (O2)
O O
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Figure 2.10c
Name andMolecularFormula
Space-FillingModel
ElectronDistribution
Diagram
Lewis DotStructure and
StructuralFormula
(c) Water (H2O)
O
H
H
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Figure 2.10d
Name andMolecularFormula
Space-FillingModel
ElectronDistribution
Diagram
Lewis DotStructure and
StructuralFormula
(d) Methane (CH4)H
C
H
HH
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Bonding capacity is called the atom’s valence
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
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Atoms in a molecule attract electrons to varying
degrees
Electronegativity is an atom’s attraction for the
electrons in a covalent bond
The more electronegative an atom is, the more
strongly it pulls shared electrons toward itself
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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
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Figure 2.11
δ−
δ−
O
δ+H
H2O
Hδ+
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Ionic Bonds
Atoms sometimes strip electrons from their bonding
partners
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
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Figure 2.12_1
Na Cl
NaSodium atom
ClChlorine atom
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Figure 2.12_2
+ −
Na Cl Na Cl
NaSodium atom
ClChlorine atom
Na+
Sodium ion(a cation)
Cl−
Chloride ion(an anion)
Sodium chloride (NaCl)
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Animation: Ionic Bonds
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A cation is a positively charged ion
An anion is a negatively charged ion
An ionic bond is an attraction between an anion and
a cation
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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
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Figure 2.13
Na+
Cl−
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Figure 2.13a
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Weak Chemical Interactions
Most of the strongest bonds in organisms are
covalent bonds that form a cell’s molecules
Many large biological molecules are held in their
functional form by weak bonds
The reversibility of weak bonds can be an advantage
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Hydrogen Bonds
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
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Figure 2.14
δ–
Water (H2O) δ–
δ+
δ+
δ–Hydrogen bond
Ammonia (NH3)
δ+ δ+
δ+
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Van der Waals Interactions
If electrons are not evenly distributed, they may
accumulate by chance in one part of a molecule
Van der Waals interactions are attractions between
molecules that are close together as a result of
these charges
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Collectively, such interactions can be strong, as
between molecules of a gecko’s toe hairs and a wall
surface
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Molecular Shape and Function
A molecule’s size and shape are key to its function
A molecule’s shape is determined by the positions of
its atoms’ orbitals
In a covalent bond, the s and p orbitals may
hybridize, creating specific molecular shapes
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Figure 2.15
Space-FillingModel
Ball-and-StickModel
Hybrid-Orbital Model(with ball-and-stick
model superimposed)
Unbondedelectronpairs H
O
H104.5º
HO
H
Water (H2O)
H
C
H
H
C
H
H
HH H
Methane (CH4)
(b) Molecular-shape models
s orbitalz
x
Three p orbitalsFour hybrid orbitals
y
Tetrahedron
(a) Hybridization of orbitals
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Figure 2.15a
s orbitalz
x
Three p orbitalsFour hybrid orbitals
y
Tetrahedron
(a) Hybridization of orbitals
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Figure 2.15b
Space-FillingModel
Ball-and-StickModel
Hybrid-Orbital Model(with ball-and-stick
model superimposed)
O
H
Water (H2O)
H
C
H
H
Methane (CH4)
(b) Molecular-shape models
104.5ºH
Unbondedelectronpairs
O
H H
H
C
H H
H
H
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Molecular shape determines how biological
molecules recognize and respond to one another
Opiates, such as morphine, and naturally produced
endorphins have similar effects because their
shapes are similar and they bind the same receptors
in the brain
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Figure 2.16
Naturalendorphin
CarbonHydrogen
NitrogenSulfurOxygen
Morphine
(a) Structures of endorphin and morphine
Naturalendorphin
Morphine
Brain cellEndorphinreceptors
(b) Binding to endorphin receptors
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Concept 2.4: Chemical reactions make and
break chemical bonds
Chemical reactions are the making and breaking of
chemical bonds
The starting molecules of a chemical reaction are
called reactants
The final molecules of a chemical reaction are called
products
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Figure 2.UN03
2 H2
Reactants
O2
Chemicalreaction
2 H2O
Products
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Photosynthesis is an important chemical reaction
Sunlight powers the conversion of carbon dioxide
and water to glucose and oxygen
6 CO2 + 6 H2O → C6H12O6 + 6 O2
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Figure 2.17
Leaf Bubbles of O2
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All chemical reactions are reversible: Products of the
forward reaction become reactants for the reverse
reaction
The two opposite-headed arrows indicate that a
reaction is reversible
3 H2 + N ⇌ 2 NH3
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Chemical equilibrium is reached when the forward
and reverse reactions occur at the same rate
At equilibrium the relative concentrations of
reactants and products do not change
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Figure 2.0
UNIT 1: THE ROLE OF CHEMISTRY IN BIOLOGY
Dr. Lovell Jones Dr. Lovell Jones in his lab, where hehas studied the relationship betweenhormones and cancers
“Studying biochemistry in a holistic way is going to be the keyto the answers we need.”
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Figure 2.0a
Dr. Lovell Jones
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Figure 2.0b
Dr. Lovell Jones in his lab, where hehas studied the relationship betweenhormones and cancers
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Figure 2.UN01a
Fra
cti
on
of
iso
top
e r
em
ain
ing
in
fo
ssil
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
00 1 2 3 4 5 6 7 8
Time before present (half-lives)
9 10
Data from R. Pinhasi et al., Revised age of late Neanderthal occupation and the end of
the Middle Paleolithic in the northern Caucasus, Proceedings of the National Academy
of Sciences USA 147:8611–8616 (2011). doi 10.1073/pnas.1018938108
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Figure 2.UN01b
Neanderthal fossils
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Figure 2.UN02
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Figure 2.UN04
Reactants
Sunlight
Products
6 O2
Oxygen
6 CO2
Carbon dioxide
6 H2O
Water
C6H12O6
Glucose
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Figure 2.UN05
Nucleus
Protons (+ charge)determine element
Neutrons (no charge)determine isotope
Electrons (− charge)form negative cloudand determinechemical behavior
Atom
+
+
−
−
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Figure 2.UN06
Singlecovalent bond
Doublecovalent bond
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Figure 2.UN07
Ionic bond
Electrontransferforms ions
Na Cl
+ −
Na Cl
NaSodium atom
ClChlorine atom
Na+
Sodium ion(a cation)
Cl−
Chloride ion(an anion)
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Figure 2.UN08
(a) (b)
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Figure 2.UN09
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Figure 2.UN10