Transcript
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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
“Somewhere in the transition from molecules to cells, we will cross the blurry boundary between nonlife and life.” (p. 28)
Knowing the vocabulary in this chapter is critical for understanding the basic chemistry that underlies all life on Earth.
Study guide for chapter 2 is available in Canvas files.
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Figure 2.1
formic acid is used by these wood ants to protect themselves against predators and microbial parasites
Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds
Organisms are composed of matter and matter is made up of elements
Matter is anything that takes up space and has mass
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 (it has emergent properties)
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Figure 2.2
Na
Sodium
Cl
Chlorine
NaCl
Sodium chloride
The emergent properties of a compound
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 (iron, iodine, copper, etc)
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Table 2.1
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 soils
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Figure 2.3
A Tiburon Mariposa lily growing on serpentine soil.
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
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
Electrons have almost no mass and can be considered as energy since they do all the work of chemical reactions.
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Figure 2.4
Cloud of negative
charge (2 electrons)
Nucleus
+
+
Electrons
?
+
+
?
(a)
(b)
Simplified models of a helium (He) atom
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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A PET scan using radioactive isotopes
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 ball bouncing down a flight
of stairs can come to rest only
on each step, not between steps.
Third shell (highest energy
level in this model)
Second shell (higher
energy level)
Energy
absorbed
First shell (lowest energy
level)
Energy
lost
(b)
Atomic
nucleus
Electron Distribution and Chemical Properties
The chemical behavior of an atom is determined by the distribution of electrons in electron shells
Valence electrons are those in the outermost shell, or valence shell
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Figure 2.7
Hydrogen
1
First
shell
Atomic mass
4.003
He
2
Atomic number
Element symbol
Electron
distribution
diagram
Helium
He
Lithium
Second
shell
Beryllium
Boron
Carbon
Nitrogen
Oxygen
Fluorine
Neon
Sodium
Third
shell
Magnesium
Silicon
Phosphorus
Sulfur
Chlorine
Argon
2
Li
3
Be
4
B
5
C
6
N
7
O
8
F
9
Ne
10
Na
11
Mg
12
AI
13
SI
14
P
15
S
16
CI
17
Ar
18
H
Aluminum
The periodic table of the elements shows the electron distribution for each element
Figure 2.7
Hydrogen
1
First
shell
Atomic mass
4.003
He
2
Atomic number
Element symbol
Electron
distribution
diagram
Helium
He
Lithium
Second
shell
Beryllium
Boron
Carbon
Nitrogen
Oxygen
Fluorine
Neon
Sodium
Third
shell
Magnesium
Silicon
Phosphorus
Sulfur
Chlorine
Argon
2
Li
3
Be
4
B
5
C
6
N
7
O
8
F
9
Ne
10
Na
11
Mg
12
AI
13
SI
14
P
15
S
16
CI
17
Ar
18
H
Aluminum
The chemical behavior of an atom is mostly determined by the valence electrons
Figure 2.7
Hydrogen
1
First
shell
Atomic mass
4.003
He
2
Atomic number
Element symbol
Electron
distribution
diagram
Helium
He
Lithium
Second
shell
Beryllium
Boron
Carbon
Nitrogen
Oxygen
Fluorine
Neon
Sodium
Third
shell
Magnesium
Silicon
Phosphorus
Sulfur
Chlorine
Argon
2
Li
3
Be
4
B
5
C
6
N
7
O
8
F
9
Ne
10
Na
11
Mg
12
AI
13
SI
14
P
15
S
16
CI
17
Ar
18
H
Aluminum
Elements with a full valence shell are chemically inert
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
These orbitals give 3-dimensional shape to atoms and facilitate in chemical bonding.
The chemical reactivity of an atom arises from the presence of unpaired electrons in one or more orbitals.
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Figure 2.8
First shell
Second shell
Neon,
with two
filled shells
(10 electrons)
First
shell
Second
shell
1s orbital
2s orbital
x
z
Three 2p orbitals
y
(a) Electron distribution
diagram
(b) Separate electron orbitals
1s, 2s, and
2p orbitals
(c) Superimposed electron orbitals
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
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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Figure 2.9_3
Hydrogen atoms (2 H)
+
+
+
+
+
+
Hydrogen
molecule (H2)
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 and
Molecular
Formula
(a) Hydrogen (H2)
Electron
Distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
Space-
Filling
Model
H
H
(b) Oxygen (O2)
O
O
(c) Water (H2O)
O
H
H
(d) Methane (CH4)
H
H
C
H
H
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
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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??
??
O
H
H
?+
?+
H2O
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_2
+
?
Na
Cl
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
Na+
Sodium ion
(a cation)
Cl?
Chloride ion
(an anion)
Sodium chloride (NaCl)
Figure 2.12_2
+
?
Na
Cl
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
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
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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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/shape 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
?–
Water (H2O)
?–
?+
?+
?–
Hydrogen bond
Ammonia (NH3)
?+
?+
?+
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
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-Filling
Model
Ball-and-Stick
Model
Hybrid-Orbital Model
(with ball-and-stick
model superimposed)
Unbonded
electron
pairs
H
O
H
104.5º
H
O
H
Water (H2O)
H
C
H
H
C
H
H
H
H
H
Methane (CH4)
(b) Molecular-shape models
s orbital
z
x
Three p orbitals
Four hybrid orbitals
y
Tetrahedron
(a) Hybridization of orbitals
Figure 2.15b
Space-Filling
Model
Ball-and-Stick
Model
Hybrid-Orbital Model
(with ball-and-stick
model superimposed)
O
H
Water (H2O)
H
C
H
H
Methane (CH4)
(b) Molecular-shape models
104.5º
H
Unbonded
electron
pairs
O
H
H
H
C
H
H
H
H
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
Natural
endorphin
Carbon
Hydrogen
Nitrogen
Sulfur
Oxygen
Morphine
(a) Structures of endorphin and morphine
Natural
endorphin
Morphine
Brain cell
Endorphin
receptors
(b) Binding to endorphin receptors
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
Chemical
reaction
2 H2O
Products
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.UN04
Reactants
Sunlight
Products
6 O2
Oxygen
6 CO2
Carbon dioxide
6 H2O
Water
C6H12O6
Glucose
Figure 2.17
Leaf
Bubbles of O2
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