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Chapter 2
Essential Chemistry for Biology
Chapter 2
• Two Lectures
Wednesday – Basic Chemistry
Friday – Biology of Water
• MasteringBiology
Sunday night – First MasteringBiology Assignment Due
Outline for Essential Chemistry
1.
Elements of Life
a.
b.
2.
Structure of Atoms
a.
b.
c.
3.
Subatomic Particles
Atoms of Life
Isotopes and ions
Chemical Bonds
a.
b.
c.
d.
4.
5.
Four most abundant elements in organisms
Importance of trace elements
Covalent Bonds
Hydrogen bonds
Ionic bonds
Hydrophobic interactions
Chemical Reactions
Water
a.
b.
Four Properties
pH and Buffers
Structural Hierarchy
Elements and Molecules
• Atoms -
building blocks of
molecules
• Elements – types of atoms
– 92 natural elements
• Molecule – composed of two or
more atoms.
• Compounds – molecules
composed of more than one
element.
+
• Emergent properties
Sodium
Chloride
Sodium Chloride
Molecular Formulas
Water
H20
Glucose C6H12O6
25 Elements Essential for Life
•
•
Calcium (Ca): 1.5%
Phosphorus (P): 1.0%
Potassium (K): 0.4%
Carbon (C):
18.5%
Sulfur (S): 0.3%
Sodium (Na): 0.2%
Chlorine (Cl): 0.2%
Magnesium (Mg): 0.1%
Most of remaining 4% just 7
elements
Remaining >0.1% are “Trace
Elements”
Hydrogen (H):
9.5%
•
96% of living matter made of
4 elements.
• Oxygen O
• Carbon C
• Hydrogen H
• Nitrogen N
Oxygen (O):
65.0%
Trace elements: less than 0.01%
Nitrogen
(N): 3.3%
Boron (B)
Manganese (Mn)
Chromium (Cr)
Cobalt (Co)
Copper (Cu)
Molybdenum (Mo)
Selenium (Se)
Silicon (Si)
Fluorine (F)
Iodine (I)
Iron (Fe)
Tin (Sn)
Vanadium (V)
Zinc (Zn)
Essential Trace Elements
Atomic Structure
• Characteristics of Particles
–
–
–
–
–
Location
Atomic Number
Atomic Mass
Atomic Charge
Atomic Volume (Size)
Nucleus
2
Protons
Nucleus
2
Neutrons
2
Electrons
2e–
Electron cloud
Structure of Typical Atoms
Rule 1
Neutral atoms have equal number of protons and
electrons
Rule 2
Typically, atoms have equal number of protons and
neutrons
Structure of typical Nitrogen Atom
Exceptions to rules
Exception to rule 1
Ions – unequal protons and electrons (electric charge)
Nitrogen atom
7 proton and 7 electron
Neutral Charge
Nitrogen ion
7 proton and 6 electron
Positive Charge
Exception to rule 2
Variable Isotopes – variable number of neutrons
6n
6p
C-12
6 proton and 6 neutron
Common non radioactive isotope
6n
8p
C-14
6 proton and 8 neutron
Rare radioactive isotope
Properties of Common Atoms
Element
Abv
Atomic #
Mass #
Valence #
Hydrogen
H
1
1
1
Carbon
C
6
12
4
Nitrogen
N
7
14
3
Oxygen
O
8
16
2
Four Chemical Bonds
• Strong Chemical Bonds
• Covalent Bonds
• Weak Chemical Bonds
• Ionic Bonds
• Hydrogen Bonds
• Other Interactions
• Hydrophobic Interactions
Ionic Bonds
Attraction between positive ions and negative ions
Covalent Bonds
Properties of Covalent Bonds
• Sharing of pair of electrons
• Strongest of chemical bonds
• Valence number
• Single, Double, and Triple
bonds
• Important for Shape of
Molecules
• Nonpolar/polar forms
Element
Valence
H
1
C
4
N
3
O
2
#
Non-Polar and
Polar Covalent Bonds
Oxygen and Nitrogen have high electronegativity
Hydrogen has low electronegativity
Hydrogen Bonds
• Attraction between a
hydrogen with a partial
positive charge and an
electronegative atom
(linked to less
electronegative atom.)
• Requires polar bonds.
• Weak Interaction
Hydrophobic vs Hydrophobic
Molecules
Measure of hydrophobicity = # of non-polar minus # of polar
Hydrophobic Interactions
Chemical Reactions
(Rearranging Chemical Bonds)
2H2 + O2
2H2O
Water and Life
Four special Properties
• Cohesion/Adhesion
• Temperature Moderation
• Significance of Floating Ice
• Solvent Properties
Other issues
• pH
Cohesion
Surface Tension
Temperature Moderation
High Specific Heat
Evaporative cooling
Floating Ice
Water’s Solvent Properties
Sodium ion
in solution
Chloride ion
in solution
Cl–
Na
Cl
–
Salt crystal
Na
Disassociation of Water
H2O
55 M
pH = -log [H+]
Conc [H+]
10-2 M
10-3 M
10-4 M
10-5 M
10-6 M
10-7 M
10-8 M
10-9 M
H+ + OH10-7 M
10-7 M
pH
2
3
4
5
6
7
8
9
Buffers
Carbonic Acid (buffer in our blood)
In response to
rise in pH
H+
H2CO3
In response to
a drop in pH
+
HCO3-