1. Essential Chemistry for Biology
Chapter 2
Essential Chemistry for Biology

2. Chapter 2 Two Lectures MasteringBiology Wednesday – Basic Chemistry
Friday – Biology of Water
MasteringBiology
Sunday night – First MasteringBiology Assignment Due

3. Outline for Essential Chemistry
Elements of Life
Four most abundant elements in organisms
Importance of trace elements
Structure of Atoms
Subatomic Particles
Atoms of Life
Isotopes and ions
Chemical Bonds
Covalent Bonds
Hydrogen bonds
Ionic bonds
Hydrophobic interactions
Chemical Reactions
Water
Four Properties
pH and Buffers

4. Structural Hierarchy

5. 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 +

6. Molecular Formulas
Water H20 Glucose C6H12O6

7. 25 Elements Essential for Life
Oxygen (O):
65.0%
96% of living matter made of
4 elements.
Oxygen O
Carbon C
Hydrogen H
Nitrogen N
Most of remaining 4% just 7 elements
Remaining >0.1% are “Trace Elements”
Calcium (Ca): 1.5%
Phosphorus (P): 1.0%
Potassium (K): 0.4%
Sulfur (S): 0.3%
Carbon (C):
18.5%
Sodium (Na): 0.2%
Chlorine (Cl): 0.2%
Magnesium (Mg): 0.1%
Trace elements: less than 0.01%
Hydrogen (H):
9.5%
Boron (B)
Manganese (Mn)
Chromium (Cr)
Molybdenum (Mo)
Cobalt (Co)
Selenium (Se)
Copper (Cu)
Silicon (Si)
(N): 3.3%
Nitrogen
Fluorine (F)
Tin (Sn)
Iodine (I)
Vanadium (V)
Iron (Fe)
Zinc (Zn)

8. Essential Trace Elements

9. Atomic Structure Characteristics of Particles 2 Protons Nucleus 2
Location
Atomic Number
Atomic Mass
Atomic Charge
Atomic Volume (Size) 2
Protons
Nucleus 2
Neutrons 2
Electrons
Nucleus
2e–
Figure 2.4 Two simplified models of a helium atom
Electron cloud 9

10. 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

11. Exceptions to rules Exception to rule 1
Ions – unequal protons and electrons (electric charge)
Exception to rule 2
Variable Isotopes – variable number of neutrons
Nitrogen atom
7 proton and 7 electron
Neutral Charge
Nitrogen ion
7 proton and 6 electron
Positive Charge
6 n
6 p
6 n
8 p
C-12
6 proton and 6 neutron
Common non radioactive isotope
C-14
6 proton and 8 neutron
Rare radioactive isotope

12. Properties of Common Atoms
Element
Abv
Atomic #
Mass #
Valence #
Hydrogen H 1
Carbon C 6 12 4
Nitrogen N 7 14 3
Oxygen O 8 16 2

13. Four Chemical Bonds Strong Chemical Bonds Weak Chemical Bonds
Covalent Bonds
Weak Chemical Bonds
Ionic Bonds
Hydrogen Bonds
Other Interactions
Hydrophobic Interactions

14. Ionic Bonds
Attraction between positive ions and negative ions

15. Covalent Bonds

16. 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
Ele-ment
Valence # H 1 C 4 N 3 O 2

17. Non-Polar and Polar Covalent Bonds
Oxygen and Nitrogen have high electronegativity
Hydrogen has low electronegativity

18. 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

19. Hydrophobic vs Hydrophobic Molecules
Measure of hydrophobicity = # of non-polar minus # of polar

20. Hydrophobic Interactions

21. Chemical Reactions (Rearranging Chemical Bonds)
2H O H2O

22. Water and Life Four special Properties Cohesion/Adhesion
Temperature Moderation
Significance of Floating Ice
Solvent Properties
Other issues pH

23. Cohesion
Surface Tension

24. Temperature Moderation
High Specific Heat
Evaporative cooling

25. Floating Ice

26. Water’s Solvent Properties
Sodium ion
in solution
Chloride ion
in solution
Cl–
Na
Na
Cl–
Salt crystal

27. Disassociation of Water
H2O H OH-
55 M M M
pH = -log [H+]
Conc [H+] pH
10-2 M 2
10-3 M 3
10-4 M 4
10-5 M 5
10-6 M 6
10-7 M 7
10-8 M 8
10-9 M 9

28. Buffers Carbonic Acid (buffer in our blood) H2CO3 H+ + HCO3-
In response to
rise in pH
H2CO H HCO3-
a drop in pH