1. Bozeman Biology – Chemical Basis of Life
Biochemistry: Atomic And Molecular Structure (This chapter is a review of physical science- we will be going through this chapter very quickly. If you have any questions ASK.
Bozeman Biology – Chemical Basis of Life

2. Element
A pure substance that is composed of only one type of atom; There are 92 natural elements
Ex: Sodium (Na), Chlorine (Cl), Hydrogen (H), Lead (Pb)

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Atoms
Basic unit of matter; smallest particle of
element with all properties of that element
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Placed side by side, 100 million atoms would make a row only about 1 centimeter long.
Atoms contain subatomic particles that are even smaller.
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The subatomic particles that make up atoms are
protons
neutrons
electrons
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Protons (+): positively charged particles in the nucleus
Neutrons (0): neutral particles (no charge) in the nucleus
Electrons (-): negatively charged particles outside the nucleus
Helium atoms contain protons, neutrons, and electrons. The positively charged protons and uncharged neutrons are bound together in the dense nucleus, while the negatively charged electrons move in the space around the nucleus.
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7. Isotopes
atom of same element w/ different number of neutrons (e.g., carbon-12, carbon-13, carbon-14)

8. Protons + Neutrons = Atomic Mass
Drawing An Atom
1) All the mass of an atom is in the center or nucleus.
2) The mass of an atom can be calculated by adding the number of protons and the number neutrons.
Ex: 6 C
12 (Atomic Mass)
Protons + Neutrons = Atomic Mass

9. Atomic Number = The # of Protons
Where can I find the number of protons?
Ex: 6 (atomic number) C 12
Atomic Number = The # of Protons

10. Atomic Mass – Atomic Number = The # of Neutrons
How do I find the number of neutrons?
Ex: 6 C 12
12 – 6 = 6 Neutrons
Atomic Mass – Atomic Number = The # of Neutrons

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Chemical Compounds
A chemical compound is a substance formed by the chemical combination of two or more elements in definite proportions.
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12. Examples of Chemical Compounds
Water H2O
Table salt NaCl
Carbon dioxide CO2
Sugar C6H12O6

13. Characteristics of Compounds
Always formed from a specific combination of elements
2. Always formed in a fixed ratio
Ex: H3O does not = water
Ex: CO4 does not = carbon dioxide

14. Characteristics of Compounds
Compounds are chemically and physically different from the elements they are made from:
Ex: Water (H2O) has different properties than hydrogen (H) or oxygen (O)

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Chemical Bonds
The atoms in compounds are held together by chemical bonds.
The electrons that are available to form bonds are called valence electrons.
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16. Bozeman Biology – Chemical Bonds: Covalent and Ionic Bonds
The main types of chemical bonds are:
Ionic bonds
Covalent bonds
Bozeman Biology – Chemical Bonds: Covalent and Ionic Bonds
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Ionic Bonds
force of attraction between oppositely charged ions (atoms that gain or lose electrons); electrons are transferred (e.g., NaCl)
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The chemical bond in which electrons are transferred from one atom to another is called an ionic bond. The compound sodium chloride forms when sodium loses its valence electron to chlorine.
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Covalent Bonds
chemical bond formed when 2 atoms combine by
sharing electrons (e.g., H2O)
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The structure that results when atoms are joined together by covalent bonds is called a molecule.
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One more bond type…Van der Waals Forces
When molecules are close together, a slight attraction can develop between the oppositely charged regions of nearby molecules.
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23. Properties of Water! Properties of Water
Bozeman Biology Water as a Polar Molecule

24. Properties of water
Six emergent properties of water contribute to Earth’s fitness for life
Cohesion/Adhesion
Surface tension
Temperature Moderation
High specific heat
Evaporative cooling
Universal solvent

25. Why do we study water properties in biology class?
About 2/3 of the mass of a cell is water!
Most life-sustaining reactions occur in water solutions

26. Water Molecule
2 atoms of hydrogen linked by covalent bonds to 1 atom oxygen (H2O)
Polar Molecule: has positive hydrogen end and negative oxygen end

27. Water is Polar
Polarity: The electrons are unevenly distributed between the Oxygen and the two Hydrogen atoms.
Oxygen has 8 protons. Each hydrogen has 1.

28. Water is Polar
The atom with more protons (Oxygen) pulls electrons away from the atom(s)
A diagram of what’s happening:

29. Water forms Hydrogen Bonds
Hydrogen Bonds: Form due to attraction between water molecules.
Not as strong as ionic/covalent bonds

30. Water forms Hydrogen Bonds
Water can form up to 4 hydrogen bonds at once
A diagram of what’s going on:

31. Hydrogen Bonds Exist Between Water Molecules
us/biology/biology1111/animat ions/hydrogenbonds.html

32. Water is Cohesive
Cohesion: Water molecules are drawn tightly together (on the surface of a lake or a pond, this forms a film, which is called surface tension)
Explains why:
Water beads on a surface (like the lab table)
Insects can walk on water

33. A Cool Example of Cohesion / Surface Tension: Water Strider Insect

34. Water is Adhesive =
Adhesion = Water adheres (sticks) to different surfaces
Ex: Measuring water in a graduated cylinder
Water adheres (sticks) to the glass more than it adheres to itself.
That’s why there is a dip in the water when you read the volume

35. Cohesion Adhesion Ex: Water Bubble Ex: Water and Paper Towels
Cohesion Video

36. Water can undergo Capillary Action
Capillary Action= Water can flow up a tube, against gravity
Ex: Plants absorbing water through their roots

37. Water is an Excellent Solvent
Water often found as part of a mixture called a solution
Solution: one substance (solute) dissolves into another (solvent); water is called the “universal solvent”
Why is this important in humans?
Salt (NaCl) in Water

38. What does ice look like at the molecular level?

39. Water is Less Dense as a Solid Which is ice and which is water?1

40. Water is Less Dense as a Solid
Ice 1

41. States of Matter
Liquid
Gas
Solid

43. Water has a High Heat Capacity
Water absorbs a lot of heat from the air without having a large temperature change
So…lakes and oceans often stabilize air temperatures
Water absorbs heat when it evaporates; this is why sweating helps us cool down!

44. So why does it take so much heat to increase the temperature of water?!
You have to break the hydrogen bonds between water molecules first!

45. Water is less dense in its solid form
Water is less dense in its solid form than it is in its liquid form (Ice floats!)
Why might it be a bad thing for ice to sink in a pond?

46. Water: The Essential Substance for Life

47. Water Has a Neutral pH
pH: measure of how acidic or basic a solution is
scale is 0 to 14
If pH = 7, then substance is neutral (not acid or base)

48. Water Has a Neutral pH
acid: forms hydrogen ions (H) in water; pH is less than 7
base: forms hydroxide ions (OH) in water; pH is greater than 7

49. Hydrophilic and Hydrophobic Substances
A hydrophobic substance
Does not have a liking for water
Nonpolar
lipids
A hydrophilic substance
Has a liking for water
Polar or ionic
Carbohydrates, salts

50. Acids and Bases
Dissociation of water molecules leads to acidic and basic conditions that affect living organisms
Organisms must maintain homeostasis in the pH of their internal and external environments

51. Effects of Changes in pH
Water can dissociate Into hydronium ions (H+ or H3O+) and hydroxide (OH-) ions
Changes in the concentration of these ions Can have a great affect on pH in living organisms H
Hydronium
ion (H3O+)
Hydroxide
ion (OH–) + –
Figure on p. 53 of water dissociating

52. Acids, Bases and pH H2O  H+ + OH-
One water molecule in 550 million naturally dissociates into a Hydrogen Ion (H+) and a Hydroxide Ion (OH-)
Hydrogen Ion Hydroxide Ion
Acid Base
H2O  H+ + OH-

53. Acid / Base Reactions
pH level determines rate & types of reactions that can take place
buffer: weak acid or base that can react with a strong acid or base to prevent sudden changes in pH
Buffers help maintain a constant pH.  A change in pH in living cells could denature proteins, DNA and other important molecules resulting in the death of the cells.

54. Acids and Bases An acid- (sour)
Is any substance that increases the hydrogen ion (H+) concentration of a solution
A base- (bitter/slippery)
Is any substance that reduces the hydrogen ion concentration of a solution (more OH- ions)

55. The pH Scale Scale goes from 0-14 with 7 neutral
The pH of a solution Is determined by the relative concentration of hydrogen ions
Difference of 10X in hydrogen ion concentration between any two pH values
Each pH unit represents a factor of 10X change in concentration
pH 3 is 10 x 10 x 10 (1000) stronger than a pH of 6
Acids have a higher number of H+ ions than a base
Acids produce H+ ion in solution
Bases produce OH- ions in solution

56. The pH scale and pH values of various aqueous solutions
Increasingly Acidic
[H+] > [OH–]
Increasingly Basic
[H+] < [OH–]
Neutral
[H+] = [OH–]
Oven cleaner 1 2 3 4 5 6 7 8 9 10 11 12 13 14
pH Scale
Battery acid
Digestive (stomach)
juice, lemon juice
Vinegar, beer, wine,
cola
Tomato juice
Black coffee Rainwater
Urine
Pure water
Human blood
Seawater
Milk of magnesia
Household ammonia
Household bleach
Figure 3.8

57. Example: For a neutral solution: [H+] is 10-7 or - log 10-7 or - (-7)

58. Acids: pH <7 etc.
Bases: pH >7 etc.
Each pH unit is a 10x change in H+

59. Comment
[H+] + [OH-] = 14
Therefore, if you know the concentration of one ion, you can easily calculate the other.

60. Buffers The internal pH of most living cells Buffers
Must remain close to pH 7
Buffers
Are substances that minimize changes in the concentrations of hydrogen and hydroxide ions in a solution
Consist of an acid-base pair that reversibly combines with hydrogen ions
Made by organisms

61. The Threat of Acid Precipitation
Refers to rain, snow, or fog with a pH lower than pH 5.6
Is caused primarily by the mixing of different pollutants with water in the air

62. Acid Rain

63. Acid Rain

64. Bozeman Biology – Acids, Bases and pH
Acid precipitation
Can damage life in Earth’s ecosystems 1 2 3 4 5 6 7 8 9 10 11 12 13 14
More acidic
Acid rain
Normal rain
More basic
Figure 3.9
Acids, Bases and pH
Bozeman Biology – Acids, Bases and pH