Chapter 2 The Chemical Context of Life. Fig. 2-3a Sodium The emergent properties of a compound.
-
Upload
luke-patterson -
Category
Documents
-
view
222 -
download
2
Transcript of Chapter 2 The Chemical Context of Life. Fig. 2-3a Sodium The emergent properties of a compound.
Chapter 2
• The Chemical Context of Life
Fig. 2-3a
Sodium
The emergent properties of a compound
Fig. 2-3b
Chlorine
The emergent properties of a compound
Fig. 2-3c
Sodium chloride
The emergent properties of a compound
Essential Elements of Life
• 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 those required by an organism in minute quantities
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Table 2-1
Concept 2.2: An element’s propertiesdepend on the structure of its atoms
• Each element consists of unique atoms
– the smallest unit of matter that still retains the properties of an element
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Subatomic Particles
• Atoms are composed of subatomic particles
– Neutrons (no electrical charge)
– Protons (positive charge)
– Electrons (negative charge)
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Neutrons and protons form the atomic nucleus
• Electrons form a cloud around the nucleus
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Cloud of negativecharge (2 electrons)
Fig. 2-5
Nucleus
Electrons
(b)(a)
Simplified models of a helium (He) atom
Atomic Number and Atomic Mass
• atomic number
– number of protons in the nucleus
• mass number
– sum of protons plus neutrons in the nucleus
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Isotopes
• Isotopes
– two atoms of the same element that differ in number of neutrons
• Radioactive isotopes
– decay spontaneously, giving off particles and energy
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Applications of radioactive isotopes:
– Dating fossils
– Tracing atoms through metabolic processes
– Diagnosing medical disorders
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-6a
Compounds includingradioactive tracer(bright blue)
Human cells
Incubators1 2 3
4 5 6
7 8 950ºC45ºC40ºC
25ºC 30ºC 35ºC
15ºC 20ºC10ºC
Humancells areincubatedwith compounds used tomake DNA. One compound islabeled with 3H.
1
2 The cells areplaced in testtubes; their DNA isisolated; andunused labeledcompounds areremoved.
DNA (old and new)
TECHNIQUE
Fig. 2-6b
TECHNIQUE
The test tubes are placed in a scintillation counter.3
Fig. 2-6c
RESULTSC
ou
nts
per
min
ute
( 1
,000
)
010 20 30 40 50
10
20
30
Temperature (ºC)
Optimumtemperaturefor DNAsynthesis
Fig. 2-7
Cancerousthroattissue
The Energy Levels of Electrons
• Energy is the capacity to cause change
• Potential energy
• the energy that matter has stored 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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-8
(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons
Third shell (highest energylevel)
Second shell (higherenergy level)
Energyabsorbed
First shell (lowest energylevel)
Atomicnucleus
(b)
Energylost
Electron Distribution and Chemical Properties
• The chemical behavior of an atom
– determined by the distribution of electrons in electron shells
• The periodic table of the elements shows the electron distribution for each element
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-9
Hydrogen
1H
Lithium
3LiBeryllium
4BeBoron
5BCarbon
6CNitrogen
7NOxygen
8O
Fluorine
9FNeon
10Ne
Helium
2HeAtomic number
Element symbol
Electron-distributiondiagram
Atomic mass
2He
4.00Firstshell
Secondshell
Thirdshell
Sodium
11NaMagnesium
12Mg
Aluminum
13AlSilicon
14SiPhosphorus
15PSulfur
16S
Chlorine
17ClArgon
18Ar
• Valence electrons
– 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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
http://www.thecatalyst.org/electabl.html
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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-10-1
Electron-distributiondiagram
(a)Neon, with two filled shells (10 electrons)
First shell Second shell
Electron-distributiondiagram
(a)
(b) Separate electronorbitals
Neon, with two filled shells (10 electrons)
First shell Second shell
1s orbital
Fig. 2-10-2
Electron-distributiondiagram
(a)
(b) Separate electronorbitals
Neon, with two filled shells (10 electrons)
First shell Second shell
1s orbital 2s orbital Three 2p orbitals
x y
z
Fig. 2-10-3
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
Fig. 2-10-4
The formation and function of molecules depend on chemical bonding between atoms
• Atoms with incomplete valence shells share electrons with other atoms
• This results in a force of attractions called a covalent bond
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Covalent Bonds
• A covalent bond
– the sharing of a pair of valence electrons by two atoms
• the shared electrons count as part of each atom’s valence shell
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-11Hydrogen
atoms (2 H)
Hydrogenmolecule (H2)
• A molecule
– two or more atoms held together by covalent bonds
• A single bond, is the sharing of one pair of electrons
• A double bond, is the sharing of two pairs of electrons
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• structural formula
– H–H
• molecular formula
– H2
Animation: Covalent BondsAnimation: Covalent Bonds
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-12a
(a) Hydrogen (H2)
Name andMolecularFormula
Electron-distribution
Diagram
Lewis DotStructure and
StructuralFormula
Space-fillingModel
Fig. 2-12b
(b) Oxygen (O2)
Name andMolecularFormula
Electron-distribution
Diagram
Lewis DotStructure and
StructuralFormula
Space-fillingModel
Fig. 2-12c
(c) Water (H2O)
Name andMolecularFormula
Electron-distribution
Diagram
Lewis DotStructure and
StructuralFormula
Space-fillingModel
Fig. 2-12d
(d) Methane (CH4)
Name andMolecularFormula
Electron-distribution
Diagram
Lewis DotStructure and
StructuralFormula
Space-fillingModel
• Covalent bonds
– form between atoms of the same element or of different elements
• A compound
– a combination of two or more different elements
• Bonding capacity is called the atom’s valence
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Electronegativity
– 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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• nonpolar covalent bond
– Electrons are shared equally
• polar covalent bond
– one atom is more electronegative
– Electrons are not shared equally
• Unequal sharing of electrons
– causes a partial positive or negative charge on the ends of a molecule
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-13
–
+ +H H
O
H2O
Ionic Bonds
• Atoms sometimes strip electrons from their bonding partners
– Example: 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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-14-1
Na Cl
NaSodium atom Chlorine atom
Cl
Fig. 2-14-2
Na Cl Na Cl
NaSodium atom Chlorine atom
Cl Na+
Sodium ion(a cation)
Cl–Chloride ion
(an anion)
Sodium chloride (NaCl)
• 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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• 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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-15
Na+
Cl–
Weak Chemical Bonds
• Strongest bonds in organisms
– covalent bonds
• Weak chemical bonds are also important
– ionic bonds
– hydrogen bonds,
• Weak chemical bonds
– reinforce shapes of large molecules
– help molecules adhere to each other
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-16
+
+
+
+
+
Water (H2O)
Ammonia (NH3)
Hydrogen bond
Van der Waals Interactions
• If electrons are distributed asymmetrically in molecules or atoms
– result in “hot spots” of positive or negative charge
• Van der Waals interactions
– attractions between molecules that are close together as a result of these charges
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Molecular Shape and Function
• A molecule’s shape is very important to its function
– determined by the positions of its atoms’ valence orbitals
– the s and p orbitals may hybridize, creating specific molecular shapes
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-17
s orbital Three porbitals
(a) Hybridization of orbitals
Tetrahedron
Four hybrid orbitals
Space-fillingModel
Ball-and-stickModel
Hybrid-orbital Model(with ball-and-stick
model superimposed)
Unbondedelectronpair
104.5º
Water (H2O)
Methane (CH4)
(b) Molecular-shape models
z
x
y
Fig. 2-17a
s orbitalz
x
y
Three porbitals
Hybridization of orbitals
Four hybrid orbitals
Tetrahedron(a)
Fig. 2-17b
Space-fillingModel
Ball-and-stickModel
Hybrid-orbital Model(with ball-and-stick
model superimposed)
Unbondedelectronpair
104.5º
Water (H2O)
Methane (CH4)
Molecular-shape models(b)
• Biological molecules
– Recognize and interact with each other with a specificity based on molecular shape
– Molecules with similar shapes can have similar biological effects
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-18a
Natural endorphin
Morphine
KeyCarbonHydrogen
NitrogenSulfurOxygen
Structures of endorphin and morphine(a)
Fig. 2-18b
Naturalendorphin
EndorphinreceptorsBrain cell
Binding to endorphin receptors
Morphine
(b)
Chemical reactions make and break chemical bonds
• Chemical reactions
– the making and breaking of chemical bonds
• Reactants
– the starting molecules of a chemical reaction
• Products
– the final molecules of a chemical reaction
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-UN2
Reactants Reaction Products
2 H2 O2 2 H2O
• Photosynthesis is an important chemical reaction
• Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen
6 CO2 + 6 H20 → C6H12O6 + 6 O2
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-19
• All chemical reactions are reversible:
– products of the forward reaction become reactants for the reverse reaction
• Some chemical reactions go to completion: all reactants are converted to products
• Chemical equilibrium
– reached when the forward and reverse reaction rates are equal
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-UN3
Nucleus
Protons (+ charge)determine element
Neutrons (no charge)determine isotope Atom
Electrons (– charge) form negative cloudand determinechemical behavior
Fig. 2-UN4
Fig. 2-UN5
Singlecovalent bond
Doublecovalent bond
Fig. 2-UN6
Ionic bond
Electrontransferforms ions
NaSodium atom
ClChlorine atom
Na+
Sodium ion(a cation)
Cl–
Chloride ion(an anion)
Fig. 2-UN7
Fig. 2-UN8
Fig. 2-UN9
Fig. 2-UN10
Fig. 2-UN11
You should now be able to:
1. Identify the four major elements
2. Distinguish between the following pairs of terms: neutron and proton, atomic number and mass number, atomic weight and mass number
3. Distinguish between and discuss the biological importance of the following: nonpolar covalent bonds, polar covalent bonds, ionic bonds, hydrogen bonds, and van der Waals interactions
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings