1. Basic Chemistry ch. 2

2. Matter and Composition of Matter
Definition: Anything that has mass and occupies space
Matter is made up of elements –An element cannot be broken down by ordinary chemical means
Atoms - are unique building blocks for each element

3. Atomic Structure Neutrons Protons No charge, In atomic nucleus
Mass = 1 atomic mass unit (amu)
Protons
Positive charge,In atomic nucleus
Mass = 1 amu

4. Atomic Structure Electrons Negative charge ,orbit nucleus Mass = 0 amu
Equal in number to protons in atom

5. Nucleus Nucleus Helium atom Helium atom Proton Neutron Electron
cloud
Figure 2.1

6. Definition: Capacity to do work or put matter into motion
Energy
Definition: Capacity to do work or put matter into motion
Types of energy:
Kinetic: energy associated with motion
Potential: stored (inactive) energy
Electrical : results from the movement of charged particles (Na+, K+)

7. Atoms of different elements contain different numbers of protons
Identifying Elements
Atoms of different elements contain different numbers of protons
Compare hydrogen, helium and lithium

8. Hydrogen (H) Helium (He) Lithium (Li) Proton Neutron Electron
Figure 2.2

9. Identifying Elements Atomic number = Mass number =
Mass numbers of atoms of an element are not all identical
Isotopes = atoms of the same element that differ in the # of neutrons they contain

10. Hydrogen (1H) Deuterium (2H) Tritium (3H) Proton Neutron Electron
Figure 2.3

11. Molecule: two or more atoms bonded together (H2 or C6H12O6)
Atoms of Elements can combine Chemically to form Molecules and Compounds
Molecule: two or more atoms bonded together (H2 or C6H12O6)
Compound:

12. Chemical Bonds
Electrons occupy up to seven electron shells (energy levels) around nucleus
Octet rule: Except for the first shell which is full with two electrons, atoms interact in order to have eight electrons in their outermost energy level (valence shell)

13. Chemically Inert Elements
Stable and unreactive
Outermost energy level fully occupied or contains eight electrons

14. (a) Chemically inert elements
Valence shell complete 8e 2e 2e
Helium (He)
Neon (Ne)
Figure 2.4a

15. Chemically Reactive Elements
Valence shell not fully occupied by electrons
Tend to gain, lose, or share electrons (form bonds) with other atoms to achieve stability

16. (b) Chemically reactive elements
Valence shell incomplete 4e 1e 2e
Hydrogen (H)
Carbon © 1e 6e 8e 2e 2e
Oxygen (O)
Sodium (Na)
Figure 2.4b

17. Attraction of opposite charges results in: An ionic bond
Ionic Bonds
Ions are formed by:
Anions (– charge) have gained one or more electrons
Cations (+ charge) have lost one or more electrons
Attraction of opposite charges results in: An ionic bond

18. + – Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+)
Chloride ion (Cl–)
Sodium chloride (NaCl)
Figure 2.5

19. Covalent Bonds
Formed by sharing of two or more valence shell electrons
Allows each atom to fill its valence shell at least part of the time

20. + Reacting atoms Resulting molecules or Hydrogen atoms Carbon atom
Molecule of
methane gas (CH4)
(a) Formation of four single covalent bonds:
Figure 2.7a

21. + Reacting atoms Resulting molecules or Oxygen atom Oxygen atom
Molecule of
oxygen gas (O2)
(b) Formation of a double covalent bond:
Figure 2.7b

22. + Reacting atoms Resulting molecules or Nitrogen atom Nitrogen atom
Molecule of
nitrogen gas (N2)
(c) Formation of a triple covalent bond:.
Figure 2.7c

23. Sharing of electrons may be equal or unequal
Covalent Bonds
Sharing of electrons may be equal or unequal
Equal sharing produces: Electrically balanced nonpolar molecules

24. Covalent Bonds
Unequal sharing by atoms with different electron-attracting abilities produces: polar covalent bonds
H2O

25. Hydrogen Bonds
Attractive force between electropositive hydrogen of one molecule and an electronegative atom of another molecule
Important in intramolecular bonds, holding a large molecule in a three-dimensional shape

26. + –
Hydrogen bond + + – – – + + + –
(a) The slightly positive ends (+) of the water molecules become aligned with the slightly negative ends (–) of other water molecules.
Figure 2.8

27. Synthesis Reactions A + B  AB Always involve bond formation Anabolic
Endergonic

28. (a) Synthesis reactions
Smaller particles are bonded
together to form larger,
molecules.
Example
Amino acids are joined to
Form protein.
Amino acid
molecules
Protein
molecule
Figure 2.9a

29. Decomposition Reactions
AB  A + B
Reverse synthesis reactions
Involve breaking of bonds
Catabolic
Exergonic

30. (b) Decomposition reactions
Bonds are broken in larger
molecules, resulting in smaller,
less complex molecules.
Example
Glycogen is broken down to release
glucose units.
Glycogen
Glucose
molecules
Figure 2.9b

31. Classes of Compounds Inorganic compounds Organic compounds
Do not contain carbon (ex. Water, salts, and many acids and bases)
Organic compounds
Contain carbon, usually large, covalently bonded (ex’s. carbohydrates, fats, proteins, nucleic acids)

32. Water
60%–80% of the volume of living cells
Most important inorganic compound in living organisms because of its properties

33. Salts
Ionic compounds that dissociate into ions in water
Ions (electrolytes) conduct electrical currents in solution

34. Acids : Proton (H+) donors (release H+ in solution)
HCl  H+ + Cl–

35. Bases: Proton acceptors (take up H+ from solution)
NaOH  Na+ + OH–

36. Acid-Base Concentration
Acid solutions contain higher amounts of H+
As [H+] increases: acidity increases
Basic solutions contain higher concentrations of OH–
As [H+] decreases (or as [OH–] increases): alkalinity increases
pH = measure of the acidity/bascisity of a solution

37. Acid-Base Concentration
Neutral solutions:
pH = 7
Contains equal numbers of H+ and OH–
Acidic solutions
 [H+],  pH
pH = 0–6.99
Basic solutions
 [H+],  pH
pH= 7.01–14

38. Sugars and starches whose building blocks = Three classes
Carbohydrates
Sugars and starches whose building blocks =
Three classes
Monosaccharides -Simple sugars containing three to seven C atoms (glucose)
Disaccharides -Double sugars that are too large to pass through cell membranes
Polysaccharides - Three/more simple sugars, e.g., starch and glycogen; not very soluble

39. Carbohydrates Functions
Primary role: Major source of cellular fuel (glucose)

40. Hexose sugars (the hexoses shown
(a) Monosaccharides
Monomers of carbohydrates
Example
Hexose sugars (the hexoses shown
here are isomers)
Example
Pentose sugars
Glucose
Fructose
Galactose
Deoxyribose
Ribose
Figure 2.15a

41. Animation: Disaccharides
(b) Disaccharides
Consist of two linked monosaccharides
Example
Sucrose, maltose, and lactose
(these disaccharides are isomers)
Glucose
Fructose
Glucose
Glucose
Galactose
Glucose
Sucrose
Maltose
Lactose
PLAY
Animation: Disaccharides
Figure 2.15b

42. Animation: Polysaccharides
(c) Polysaccharides
Long branching chains (polymers) of linked monosaccharides
Example
This polysaccharide is a simplified representation of
glycogen, a polysaccharide formed from glucose units.
Glycogen
PLAY
Animation: Polysaccharides
Figure 2.15c

43. Lipids Insoluble in water Main types: Triglycerides Phospholipids
Steroids

44. Defined as:solid fats and liquid oils
Triglycerides
Defined as:solid fats and liquid oils
Building blocks = three fatty acids bonded to a glycerol molecule
Main functions
Energy storage
Insulation
Protection

45. (a) Triglyceride formation+
Glycerol
3 fatty acid chains
Triglyceride,
or neutral fat
3 water
molecules
Figure 2.16a

46. Similar to triglycerides:
Phospholipids
Similar to triglycerides:
Building blocks = Glycerol + two fatty acids and a phosphorus (P)-containing group
“Head” and “tail” regions have different properties
Important in cell membrane structure

47. (b) “Typical” structure of a phospholipid molecule
Two fatty acid chains and a phosphorus-containing group are
attached to the glycerol backbone.
Example
Phosphatidylcholine
Polar
“head”
Nonpolar
“tail”
(schematic
phospholipid)
Phosphorus-
containing
group (polar
“head”)
Glycerol
backbone
2 fatty acid chains
(nonpolar “tail”)
Figure 2.16b

48. Steroids
Steroids—interlocking four-ring structure
Examples are cholesterol, vitamin D, steroid hormones, and bile salts

49. Simplified structure of a steroid
Four interlocking hydrocarbon rings form a steroid.
Example
Cholesterol (cholesterol is the
basis for all steroids formed in the body)
Figure 2.16c

50. Proteins Building blocks = amino acids
After amino acids are linked together they often undergo a natural folding process
This folding process results in four different levels of protein structure: primary, secondary, tertiary, quaternary

51. this amino acid is likely intramolecular bonding.
Amine
group
Acid
group
(a) Generalized
structure of all
amino acids.
(b) Glycine is the simplest
amino acid.
(c) Aspartic acid
(an acidic amino acid)
has an acid group
(—COOH) in the
R group.
(d) Lysine
(a basic amino acid)
has an amine group
(–NH2) in the R group.
(e) Cysteine
(a basic amino acid)
has a sulfhydryl (–SH)
group in the R group,
which suggests that
this amino acid is likely
to participate in
intramolecular bonding.
Figure 2.17

52. Animation: Primary Structure
Amino acid
Amino acid
Amino acid
Amino acid
Amino acid
(a) Primary structure:
The sequence of amino acids forms the polypeptide chain.
PLAY
Animation: Primary Structure
Figure 2.19a

53. Animation: Secondary Structure
a-Helix:
b-Sheet:
(b) Secondary structure:
The primary chain forms spirals (a-helices) and sheets (b-sheets).
PLAY
Animation: Secondary Structure
Figure 2.19b

54. Animation: Tertiary Structure
(c) Tertiary structure:
PLAY
Animation: Tertiary Structure
Figure 2.19c

55. Animation: Quaternary Structure
(d) Quaternary structure:
Two or more polypeptide chains, each with its own tertiary structure,
combine to form a functional protein.
PLAY
Animation: Quaternary Structure
Figure 2.19d

56. Protein Denaturation
Shape change and disruption of active sites due to environmental changes
A denatured protein is nonfunctional

57. Enzymes Are proteins Biological catalysts
Increase the speed of a reaction
Allows for millions of reactions/minute

58. Enzyme Function
Substrates +
Active site
Enzyme

59. Nucleic Acids
DNA and RNA
Building blocks = nucleotide, composed of N-containing base, a pentose sugar, and a phosphate group

60. Deoxyribonucleic Acid (DNA)
Four Nitrogen containing bases:
adenine (A), guanine (G), cytosine (C), and thymine (T)
Double-stranded, helical
Replicates before cell division, ensuring genetic continuity
Provides instructions for protein synthesis

61. (c) Computer-generated image of a DNA molecule
Sugar:
Deoxyribose
Base:
Adenine (A)
Phosphate
Thymine (T)
Sugar
Phosphate
Adenine nucleotide
Thymine nucleotide
Hydrogen
bond
(a)
Deoxyribose
sugar
Sugar-phosphate
backbone
Phosphate
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
(b)
(c) Computer-generated image of a DNA molecule
Figure 2.22

62. Ribonucleic Acid (RNA)
Four bases:
adenine (A), guanine (G), cytosine (C), and uracil (U)
Single-stranded
PLAY
Animation: DNA and RNA

63. Adenosine Triphosphate (ATP)
Adenine-containing RNA nucleotide with two additional phosphate groups

64. High-energy phosphate bonds can be hydrolyzed to release energy.
Adenine
Phosphate groups
Ribose
Adenosine
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)
Figure 2.19

65. Function of ATP Phosphorylation:
The chemical energy contained in the high energy phosphate bonds can be used to perform cellular work

66. Figure 2.20 Solute + Membrane protein (a) Transport work +
Relaxed smooth
muscle cell
Contracted smooth
muscle cell
(b)
Mechanical work +
(c)
Chemical work
Figure 2.20