Transcript The Chemical Context of Life Atoms, Bonding, Molecules

Lecture 2
8/31/05
The Chemical Context of Life
Atoms, Bonding, Molecules
Before we start…
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Questions from last time?
Elements
Matter
Compounds
Bonded Elements
Pure substances
Made up of two or more
Types of atoms bonded together
In a fixed ratio
NEW SUBSTANCE
Different Properties
Made up of only One
type of atom
+
Figure 2.2
Sodium
Chloride
Sodium Chloride
ATOMS are the smallest unit of
matter that maintain the properties of
an element
Why ATOMS bond together chemically
is because of their subatomic
structure
Basis for Chemical Bonding
Atomic Structure
Atomic number = protons
Protons (+)
Neutrons (o)
Atomic mass =
protons + neutrons
nucleus
Electrons
(-)
Electron number
Chemical
properties
Atoms are electrically neutral !
Atoms differ by the number
of protons and electrons
Atomic“character”
Electrons are arranged in SHELLS
1 outer
shell electron
4 outer
shell electrons
1 outer
shell electron
7 outer
shell electrons
Character determined by
Outer Shell Electrons
• The periodic table of the elements
– Shows the electron distribution for all the
elements
Hydrogen
1H
Atomic mass
First
shell
2
He
4.00
Atomic number Helium
2He
Element symbol
Electron-shell
diagram
Lithium
3Li
Beryllium
4Be
Boron
3B
Carbon
6C
Nitrogen
7N
Oxygen Fluorine
8O
9F
Neon
10Ne
Second
shell
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur
13Al
16S
11Na
12Mg
14Si
15P
Third
shell
Figure 2.8
Chlorine
17Cl
Argon
18Ar
Bonding: achieve electronic stability
“full outer shells of electrons”
Ionic Bonding
“Theft”
Covalent Bonding
“Sharing
What determines
Ionic or Covalent Bonding?
Electronegativity
• Electronegativity
– Is the attraction of a particular kind of atom
for the electrons in a covalent bond
• The more electronegative an atom
– The more strongly it pulls shared electrons
toward itself
Ionic bonding
Atoms have very different
electronegativities
Hydrogen
1H
Atomic mass
First
shell
Figure 2.8
Beryllium
4Be
Boron
3B
Weak
ElectroNegativity
Sodium Magnesium Aluminum
Nearly
Al
Na
Mg
Empty
Outer
Shells
11
Third
shell
Atomic number Helium
2He
Element symbol
Electron-shell
diagram
Lithium
3Li
Second
shell
2
He
4.00
12
13
Carbon
6C
Nitrogen
7N
Silicon Phosphorus
14Si
15P
Electronically
Stable
Oxygen Fluorine Neon
Full
8O
10Ne
9F
Strong
Outer
ElectroShells
NONNegative
Chlorine Argon
Sulfur
REACTIVE
S
17Cl
18Ar
Nearly
16
Full
Outer
shells
Ionic Bonding:“Theft & Abandonment”
(Na)
(Cl)
Unfilled outer shells
Electronically neutral
(Na+)
(Cl-)
Filled outer shells
CHARGED SPECIES
No longer atoms:
IONS
Attraction between ions
is very strong
• An anion
– Is negatively charged ions
• A cation
– Is positively charged
• An ionic bond
– Is an attraction between anions and cations
2
1
The lone valence electron of a sodium
atom is transferred to join the 7 valence
electrons of a chlorine atom.
Each resulting ion has a completed
valence shell. An ionic bond can form
between the oppositely charged ions.
–
+
Na
Na
Sodium atom
(an uncharged
atom)
Figure 2.13
Cl
Cl
Chlorine atom
(an uncharged
atom)
Cl
Na
Na+
Sodium on
(a cation)
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)
• Ionic compounds
– Are often called salts, which may form
crystals
Na+
Cl–
Figure 2.14
Covalent Bonding: sharing between
atoms of similar electronegativity
Hydrogen
1H
Atomic mass
First
shell
Element symbol
Electron-shell
diagram
Lithium
3Li
Second
shell
Atomic number Helium
2He
2
He
4.00
Beryllium
4Be
Boron
3B
Intermediate
Nitrogen Oxygen
ElectroO
N
Negativity
Carbon
6C
7
8
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur
13Al
16S
11Na
12Mg
14Si
15P
Third
shell
Figure 2.8
Fluorine
9F
Neon
10Ne
Chlorine
17Cl
Argon
18Ar
Covalent Bonding: “Sharing”
Same electronegativity
H
H
• physical overlap
between atoms
• full outer shells
• physically tied at
the hip
H-H
H2
• geometrical/spatial
orientation fixed
MOLECULES
Name
(molecular
formula)
(c) Water (H2O).
Two hydrogen
atoms and one
oxygen atom are
joined by covalent
bonds to produce a
molecule of water.
(d) Methane (CH4).
Four hydrogen
atoms can satisfy
the valence of
one carbon
atom, forming
methane.
Electronshell
diagram
Structural
formula
O
Spacefilling
model
H
H
H
H
C
H
H
Figure 2.11 C, D
Specific Geometry
• Each electron shell
– Consists of a specific number of orbitals
– Orbitals are defined areas of space that
electrons occupy within electron shells
Electron orbitals.
Each orbital holds
up to two electrons.
x
Y
Z
1s orbital
2s orbital
Three 2p orbitals
1s, 2s, and 2p orbitals
Electron-shell diagrams.
Each shell is shown with
its maximum number of
electrons, grouped in pairs.
Figure 2.9
(a) First shell
(maximum
2 electrons)
(b) Second shell
(maximum
8 electrons)
(c) Neon, with two filled shells
(10 electrons)
• In a covalent bond
– The s and p orbitals may hybridize, creating
specific molecular shapes
Three p orbitals
Z
s orbital
Four hybrid orbitals
X
Y
Tetrahedron
(a) Hybridization of orbitals. The single s and three p orbitals
of a valence shell involved in covalent bonding combine to
form four teardrop-shaped hybrid orbitals. These orbitals
extend to the four corners of an imaginary tetrahedron
Figure 2.16 (a) (outlined in pink).
Space-filling
model
Ball-and-stick
model
Hybrid-orbital model
(with ball-and-stick
model superimposed)
Unbonded
Electron pair
O
O
H
Water (H2O)
104.5°
H
H
H
H
C
C
H
H
Methane (CH4)
H
H
H
H
H
(b) Molecular shape models. Three models representing molecular shape are shown for
two examples; water and methane. The positions of the hybrid orbital determine the
Figure 2.16 (b)
shapes of the molecules
COVALENT BONDING:
Sharing
Products of Covalent bonding are called
MOLECULES
• A molecule
– Consists of two or more atoms held together by
covalent bonds
• A single bond
– Is the sharing of one pair of valence electrons
• A double bond
– Is the sharing of two pairs of valence electrons
• Single and double covalent bonds
Name
(molecular
formula)
(a) Hydrogen (H2).
Two hydrogen
atoms can form a
single bond.
(b) Oxygen (O2).
Two oxygen atoms
share two pairs of
electrons to form
a double bond.
Figure 2.11 A, B
Electronshell
diagram
Structural
formula
H
H
O
O
Spacefilling
model
Missing: 2
makes
water
4
outer shell electrons
Valence
Electrons
always
3
2
3
cytosine
4
bonds
Molecular Shape and Function
• The precise shape of a molecule
– Is usually very important to its function
in the living cell
– Is determined by the positions of its
atoms’ valence orbitals
• Molecular shape
– Determines how biological molecules
recognize and respond to one another
with specificity
Carbon
Nitrogen
Hydrogen
Sulfur
Oxygen
Natural
endorphin
Morphine
(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to
receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.
Natural
endorphin
Brain cell
Figure 2.17
Morphine
Endorphin
receptors
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.
Two Types of Covalent Bonds
• nonpolar covalent bond
– The atoms have similar
electronegativities
– Share the electron equally
•polar covalent bond
-The atoms have fairly different
electronegativities
- Share the electrons, but unequally
• polar covalent bond
– The atoms have differing electronegativities
– Share the electrons unequally
Water
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
d–
This results in a
partial negative
charge on the
oxygen and a
partial positive
charge on
the hydrogens.
O
Figure 2.12
d+
H
H
H2O
d+
POLAR COVALENT BOND
the sharing of electrons in a bond is unequal
negative pole
the molecule is
LOPSIDED
NO NET CHARGE
JUST ASYMMETRY
positive pole
Asymmetry of Electrons within Water
has some interesting Consequences
Individual Water Molecules have
Considerable attraction for one another
Cohesion / Cohesive Properties
Water molecules act as little magnets
+
Electron withdrawing
Hydrogen Bonds
weak, dynamic,
electrostatic interactions
* additive
Dipole
S
N
S
N
S
+
N
+
+
+
+
+
+
+
• The polarity of water molecules
– Allows them to form hydrogen bonds with
each other
– Contributes to the various properties water
exhibits
d–
Hydrogen
bonds
+
H
+
d–
d–
+
Figure 3.2
H
+
d–
Properties of water due to Polarity
1. Cohesion/surface tension
2. Temperature moderation
• High specific heat
• Evaporative cooling
• Ice floats
3. Solvent Ability
• Hydrophilicity and hydrophobicity
4. Ionization ability (pH)
Summary Points of Lecture 2
• Atomic Structure
• Atoms bond to achieve full outer electron shells
• Ionic bonding “theft and abandonment”
- consequence: IONS, charged species
- Consequence: strong attraction of ions
•Covalent Bonding “sharing”
- consequence: molecules
- consequence: atoms physically tied at the hip
- consequence: precise 3-D spatial geometries
• POLAR Covalent Molecules
- Asymmetric charge distribution within molecule
- “little magnets”
- water is most common example
3
Emergent properties of water
contribute to Earth’s fitness for life
1. Cohesion - water molecules stick to one another
Water conducting cells
Figure 3.4
100 µm
Surface
Tension
Gas = Steam
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Liquid
+
+
+
+
Emergent properties of water
contribute to Earth’s fitness for life
2. Temperature Moderation
- water has a high specific heat
(energy to raise 1g of substance 1oC)
- heat is absorbed when Hydrogen bonds break
- heat is released when Hydrogen bonds form
- keeps temperature of earth from fluctuating wildly
- heat capacities in change of state (solid-liquid-gas)
(heat of vaporization, heat of fusion)
Gas = Steam
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Liquid
+
+
+
+
Some consequences Water hydrogen bonding
• Evaporative cooling
– Is due to water’s high heat of
vaporization
– Allows water to cool a surface
• Solid Water – ICE
Is less dense than Water – SO FLOATS
- Insulates bodies of water
• The hydrogen bonds in ice
– Are more “ordered” than in liquid water,
making ice less dense
Hydrogen
bond
Figure 3.5
Ice
Liquid water
Hydrogen bonds are stable
Hydrogen bonds
constantly break and re-form
The Solvent of Life
• Water is a versatile solvent due to its
polarity
• It can form aqueous solutions
• The different regions of the polar water
molecule can interact with ionic compounds
called solutes and dissolve them
Negative
oxygen regions
of polar water molecules
are attracted to sodium
cations (Na+).
Positive
hydrogen regions
of water molecules
cling to chloride anions
(Cl–).
–
Na+
+
–
–
Na+
Cl–
+
Cl –
–
+
+
–
Figure 3.6
–
+
+
–
–
+
+
–
–
• Water can also interact with polar molecules
such as proteins
This oxygen is
attracted to a slight
d– positive charge on
the lysozyme
d+
molecule.
This oxygen is attracted to a slight
negative charge on the lysozyme molecule.
(a) Lysozyme molecule
in a nonaqueous
Figure 3.7
environment
(b) Lysozyme molecule (purple)
in an aqueous environment
such as tears or saliva
(c) Ionic and polar regions on the protein’s
Surface attract water molecules.