1. Chapter 2: The Chemical Level of Organization

2. Introduction to Chemistry
Matter is made up of atoms
Atoms join together to form chemicals with different characteristics
Chemical characteristics determine physiology at the molecular and cellular level

3. Atomic Particles Proton: Neutron: Electron: positive, 1 mass unit
neutral, 1 mass unit
Electron:
negative, low mass

4. Particles and Mass Atomic number: Mass number: Atomic weight:
number of protons
Mass number:
number of protons plus neutrons
Atomic weight:
exact mass of all particles (daltons)

5. Isotopes
2 or more elements with equal numbers of protons but different numbers of neutrons
Electron
shell p+ p + n e
Hydrogen-1
(electron-shell model)
(b) Hydrogen-2
deuterium
(c) Hydrogen-3,
tritium

6. Elements in the Human Body
Table 2–1

7. How do atoms form molecules and compounds?

8. Molecules and Compounds
atoms joined by strong bonds
Compounds:
atoms joined by strong or weak bonds

9. Chemical Bonds Ionic bonds: Covalent bonds: Hydrogen bonds:
attraction between cations (+) and anions (-)
Covalent bonds:
strong electron bonds
Non polar covalent bonds: equal sharing of electrons
Polar covalent bonds: unequal sharing of electrons
Hydrogen bonds:
weak polar bonds

10. Ionic Bonds
Are atoms with positive or negative charge
Figure 2–3a

11. Electron-Shell Model and
Covalent Bond
Formed between atoms that share electrons
Hydrogen
(H2)
Oxygen
(O2)
Carbon
Dioxide
(CO2)
Nitric
Oxide
(NO)
Molecule
Electron-Shell Model and
Structural Formula
H–H
O=O
N=O
O=C=O
Free Radicals:
Ion or molecule that
contain unpaired
electrons in the outermost
shell.
- Extremely Reactive
-Typically enter into
destructive reactions
-Damage/destroy vital
compounds

12. Hydrogen Bonds Attractive force between polar covalent molecules
Weak force that holds molecules together
Hydrogen bonds between H2O molecules cause surface tension
Figure 2–6

13. How is it possible for two samples of hydrogen to contain the same number of atoms, yet have different weights?
A. One sample has more bonds.
B. One sample contains fewer electrons, decreasing weight.
C. One sample contains more of hydrogen’s heavier isotope(s).
D. One sample includes more protons, increasing weight.

14. Both oxygen and neon are gases at room temperature
Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does not. Why?
A. Neon has 8 electrons in its valence shell, oxygen has only 6.
B. Neon cannot undergo bonding due to its polarity.
C. Neon is exergonic.
D. Neon’s molecular weight is too low to allow bonding.

15. Both oxygen and neon are gases at room temperature
Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does not. Why?
A. Neon has 8 electrons in its valence shell, oxygen has only 6.
B. Neon cannot undergo bonding due to its polarity.
C. Neon is exergonic.
D. Neon’s molecular weight is too low to allow bonding.

16. Which kind of bond holds atoms in a water molecule together
Which kind of bond holds atoms in a water molecule together? What attracts water molecules to one another?
A. polar covalent bonds; hydrogen bonds
B. ionic bonds; charge interactions
C. hydrogen bonds; charge interactions
D. covalent bonds; hydrogen bonds

17. Why are chemical reactions important to physiology?

18. Energy Energy: Work: the capacity to do work
a change in mass or distance

19. Forms of Energy Kinetic energy: Potential energy: Chemical energy:
energy of motion
Potential energy:
stored energy
Chemical energy:
potential energy stored in chemical bonds
When energy is exchanged, heat is produced
- cells cannot capture it or use it for work

20. Break Down, Build Up Decomposition reaction (catabolism): AB A + B
Synthesis reaction (anabolism):
A + B AB
Exchange reaction (reversible):
AB + CD AD + CB
If Water is Involved:
Hydrolysis:
A—B—C—D—E + H2O A—B—C—H + HO—D—E
Dehydration synthesis (condensation):
A—B—C—H + HO—D—E A—B—C—D—E + H2O

21. KEY CONCEPT
Reversible reactions seek equilibrium, balancing opposing reaction rates
Add or remove reactants:
reaction rates adjust to reach a new equilibrium

22. How do enzymes control metabolism?

23. Activation Energy
Chemical reactions in cells cannot start without help
Activation energy gets a reaction started
Figure 2–7

24. Materials in Reactions
Reactants:
materials going into a reaction
Products:
materials coming out of a reaction
Enzymes:
proteins that lower the activation energy of a reaction

25. Energy In, Energy Out Exergonic reactions: Endergonic reactions:
produce more energy than they use
Heat will be the by-product
Endergonic reactions:
use more energy than they produce
Most chemical reactions that sustain life cannot occur unless the right enzymes are present

26. How would you classify this reaction?
In cells, glucose, a six-carbon molecule, is converted into two three-carbon molecules by a reaction that releases energy.
How would you classify this reaction?
A. endergonic
B. exergonic
C. decomposition
D. B and C

27. How would you classify this reaction?
In cells, glucose, a six-carbon molecule, is converted into two three-carbon molecules by a reaction that releases energy.
How would you classify this reaction?
A. endergonic
B. exergonic
C. decomposition
D. B and C

28. Why are enzymes needed in our cells?
A. to promote chemical reactions
B. for chemical reactions to proceed
under conditions compatible with
life
C. to lower activation energy
requirements
D. all of the above

29. What is the difference between organic and inorganic compounds?

30. Organic and Inorganic Molecules
molecules based on carbon and hydrogen
Inorganic:
molecules not based on carbon and hydrogen

31. Essential Molecules Nutrients: Metabolites:
essential molecules obtained from food
Metabolites:
molecules made or broken down in the body

32. Why is water so important to life?

33. Properties of Water Solubility: Reactivity: High heat capacity:
water’s ability to dissolve a solute in a solvent to make a solution
Reactivity:
most body chemistry uses or occurs in water
High heat capacity:
water’s ability to absorb and retain heat
Lubrication:
to moisten and reduce friction
Water is the key structural and functional component of cells and their control mechanisms, the nucleic acids

34. Aqueous Solutions Polar water molecules form hydration
spheres around ions and small polar molecules
to keep them in solution
Figure 2–8

35. Electrolytes Inorganic ions: conduct electricity in solution
Electrolyte imbalance seriously disturbs vital body functions

36. Molecules and Water Hydrophilic: Hydrophobic:
hydro = water, philos = loving
reacts with water
Hydrophobic:
phobos = fear
does not react with water

37. Solutions Suspension: Concentration:
a solution in which particles settle (sediment)
Concentration:
the amount of solute in a solvent (mol/L, mg/mL)

38. What is pH and why do we need buffers?

39. pH: Neutral, Acid, or Base?
the concentration of hydrogen ions (H+) in a solution
Neutral pH:
a balance of H+ and OH—
pure water = 7.0
Acid (acidic): pH lower than 7.0
high H+ concentration, low OH— concentration
Base (basic): pH higher than 7.0
low H+ concentration, high OH— concentration

40. pH Scale Has an inverse relationship with H+ concentration:
more H+ ions mean lower pH, less H+ ions mean higher pH
Figure 2–9

41. KEY CONCEPT pH of body fluids measures free H+ ions in solution
Excess H+ ions (low pH): Acidosis
damages cells and tissues
alters proteins
interferes with normal physiological functions
Excess OH— ions (high pH): Alkalosis
Uncontrollable and sustained skeletal muscle contractions

42. Controlling pH Salts: Buffers: positive or negative ions in solution
contain no H+ or OH— (NaCl)
Buffers:
weak acid/salt compounds
neutralizes either strong acid or strong base

43. Why does a solution of table salt conduct electricity, but a sugar solution does not?
A. Electrical conductivity requires ions.
B. Sugar forms a colloid, salt forms a suspension.
C. Electricity is absorbed by glucose molecules.
D. Table salt is hydrophobic, sugar is hydrophilic.

44. How does an antacid help decrease stomach discomfort?
A. by reducing buffering capacity of the stomach
B. by decreasing pH of stomach contents
C. by reacting a weak acid with a stronger one
D. by neutralizing acid using a weak base

45. What kinds of organic compounds are there, and how do they work?

46. Functional Groups of Organic Compounds
Molecular groups which allow molecules to interact with other molecules
Table 2–4

47. Carbohydrates Consist of C:H:O in 1:2:1 ratio 1. Monosaccharides:
simple sugars with 3 to 7 carbon atoms (glucose)
Glucose: important metabolic fuel
2. Disaccharides:
2 simple sugars condensed by dehydration synthesis (sucrose)

48. Simple Sugars Structural Formula: Straight-chain form Ring from 3-D
Isomers: Glucose vs. Fructose:
- Same chemical formula
but different shape
Figure 2–10

49. Polysaccharides Chains of many simple sugars (glycogen) Formation:
Dehydration synthesis
Breakdown:
Hydrolysis synthesis
Glycogen: made and stored in muscle cells
Figure 2–12

50. Carbohydrate Functions
Polysaccharides
Glycogen: made and stored in muscle cells
Cellulose: structural component of plants
-Ruminant Animals: Cattle, sheep, and deer
Table 2–5

51. The Ruminant Stomach
Ruminant stomach is polygastric: four compartments
-Rumen Reticulum
-Abomasum Omasum

52. Rumen Occupies 80% of the stomach Muscular Pillar
Contract to mix feed
Digest starch and fibers
Microbes produce VFA’s
Lined with Papillae
pH of
Provide a suitable environment for bacteria and protozoa

53. KEY CONCEPT
Carbohydrates are quick energy sources and components of membranes
Lipids have many functions, including membrane structure and energy storage
Provides 2x more energy then carbohydrates

54. Lipids Mainly hydrophobic molecules such as fats, oils, and waxes
Made mostly of carbon and hydrogen atoms (1:2), and some oxygen
Less oxygen then carbon

55. Classes of Lipids Fatty acids Eicosanoids Glycerides Steroids
Phospholipids and glycolipids

56. Fatty Acids Carboxyl group -COOH Hydrocarbon tail:
Hydrophilic
Hydrocarbon tail:
Hydrophobic
Longer tail = lower solubility
Saturated vs. Unsaturated
Saturated: solid at room temp.
Cause solid plaques in arteries
Unsaturated: liquid at room temp.
Healthier
Figure 2–13

57. Eicosanoids Used for cellular communication Never burned for energy
1. Leukotrienes:
active in immune system
Used by cells to signal injury
2. Prostaglandins: local hormones
Used for cell-to-cell signaling to coordinate events

58. Steroids 4 carbon ring with attached carbon chains
Not burned for energy
Figure 2–16

59. Types of Steroids Cholesterol: Estrogens and testosterone:
cell membrane formation and maintenance, cell division, and osmotic stability
Estrogens and testosterone:
Regulation of sexual function
Corticosteroids and calcitrol:
Tissue metabolism and mineral balance
Bile salts:
Processing of dietary fats

60. Glycerides
Glycerides: are the fatty acids attached to a glycerol molecule
Triglyceride: are the 3 fatty-acid tails, fat storage molecule
Fat Deposits are Important
Energy Storage
Insulation
Mechanical Protection
-Knees and Eye Sockets
Figure 2–15

61. Phospholipids Vs. Glycolipids Combination Lipids
Cell Membranes are Composed of these lipids
Hydrophilic
Diglyceride
Hydrophobic
Figure 2–17a, b

62. Phospholipids Vs. Glycolipids Combination Lipids
Spontaneous formation of Micelle
Figure 2–17c

63. 5 Lipid Types
Table 2–6

64. A food contains organic molecules with the elements C, H, and O in a ratio of 1:2:1. What class of compounds do these molecules belong to, and what are their major functions in the body?
A. lipids; energy source
B. proteins; support and movement
C. nucleic acids; determining inherited characteristics
D. carbohydrates; energy source

65. When two monosaccharides undergo a dehydration synthesis reaction, which type of molecule is formed?
A. polypeptide
B. disaccharide
C. eichosanoid
D. polysaccharide

66. Which kind of lipid would be found in a sample of fatty tissue taken from beneath the skin?
A. eichosanoid
B. steroid
C. triglyceride
D. phospholipid

67. Which lipids would you find in human cell membranes?
A. cholesterol
B. glycolipids
C. phospholipids
D. all of the above

68. Protein Structure
Proteins are the most abundant and important organic molecules
Basic elements:
carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)
Basic building blocks:
20 amino acids

69. Protein Functions 7 major protein functions:
support: structural proteins
movement: contractile proteins
transport: transport proteins
buffering: regulation of pH
metabolic regulation: enzymes
coordination and control: hormones
defense: antibodies

70. Proteins
Proteins:
control anatomical structure and physiological function
determine cell shape and tissue properties
perform almost all cell functions

71. Amino Acid Structure central carbon hydrogen amino group (—NH2)
carboxylic acid group (—COOH)
variable side chain or R group
Figure 2-18

72. Peptide Bond A dehydration synthesis between: amino group of 1
amino acid
and the carboxylic acid group of another amino acid
producing a peptide

73. Primary Structure Polypeptide: Linear sequence of amino acids
How many amino acids were bound together
What order they are bound
Figure 2–20a

74. Secondary Structure
Hydrogen bonds form spirals or pleats
Figure 2–20b

75. Tertiary Structure Secondary structure folds into a unique shape
Global coiling or folding due to R group interaction
Figure 2–20c

76. Quaternary Structure Final protein shape: Fibrous proteins:
several tertiary structures together
Fibrous proteins:
- structural sheets
Globular proteins:
- soluble spheres
with active functions
Figure 2–20d

77. Shape and Function Protein function is based on shape
Shape is based on sequence of amino acids
Denaturation:
loss of shape and function due to heat or pH

78. Enzymes Enzymes are catalysts:
proteins that lower the activation energy of a chemical reaction
are not changed or used up in the reaction

79. How Enzymes Work Substrates: reactants in enzymatic reactions
Active site: location on an enzyme that fits a
particular substrate
Figure 2–21

80. Enzyme Helpers Cofactor: Coenzyme: Isozymes:
an ion or molecule that binds to an enzyme before substrates can bind
Coenzyme:
nonprotein organic cofactors (vitamins)
Isozymes:
2 enzymes that can catalyze the same reaction

81. Enzyme Characteristics
Specificity:
one enzyme catalyzes one reaction
Saturation limits:
an enzyme’s maximum work rate
Regulation:
the ability to turn off and on

82. Conjugated Protein Glycoproteins: Proteoglycans:
large protein + small carbohydrate
includes enzymes, antibodies, hormones, and mucus production
Proteoglycans:
large polysaccharides + polypeptides
promote viscosity

83. Proteins are chains of which small organic molecules?
A. saccharides
B. fatty acids
C. amino acids
D. nucleic acids

84. Which level of protein structure would be affected by an agent that breaks hydrogen bonds?
A. the primary level of protein structure
B. the secondary level of protein structure
C. the tertiary level of protein structure
D. the protein structure would NOT be affected by this agent

85. Why does boiling a protein affect its structural and functional properties?
A. Heat denatures the protein, causing unfolding.
B. Heat causes the formation of additional quaternary structure.
C. Heating rearranges the primary structure of the protein.
D. Heat alters the radical groups on the amino acids.

86. Why does boiling a protein affect its structural and functional properties?
A. Heat denatures the protein, causing unfolding.
B. Heat causes the formation of additional quaternary structure.
C. Heating rearranges the primary structure of the protein.
D. Heat alters the radical groups on the amino acids.

87. How might a change in an enzyme’s active site affect its functions?
A. increased activity due to a better fit with the substrate
B. decreased activity due to a poor substrate fit
C. inhibited activity due to no substrate fit
D. all of the above

88. Nucleic Acids C, H, O, N, and P
Large organic molecules, found in the nucleus, which store and process information at the molecular level
DNA – deoxyribonucleic acid
RNA – ribonucleic acid

89. DNA and RNA DNA Determines inherited characteristics
Directs protein synthesis
Controls enzyme production
Controls metabolism
RNA
Codes intermediate steps in protein synthesis

90. KEY CONCEPT
DNA in the cell nucleus contains the information needed to construct all of the proteins in the body

91. Nucleotides Are the building blocks of DNA Have 3 molecular parts:
sugar (deoxyribose)
phosphate group
nitrogenous base (A, G, T, C)

92. The Bases
Figure 2–22b, c

93. Complementary Bases Purines pair with pyrimidines: DNA: RNA:
adenine (A) and thymine (T)
cytosine (C) and guanine (G)
RNA:
uracil (U) replaces thymine (T)

94. RNA and DNA RNA: DNA: a single strand
a double helix joined at bases by hydrogen bonds

95. Protein Synthesis: Three forms of RNA
messenger RNA (mRNA)
Protein blueprint or instructions
transfer RNA (tRNA)
Carry amino acids to the place where proteins are being synthesized
ribosomal RNA (rRNA)
Forms the site of protein synthesis in the cell
Factory = ribosomes

96. High-Energy Compounds: ADP and ATP
- Assembled using RNA Nucleotides
- Bonds are broken easily by cells to release energy as needed
During digestion and cellular respiration:
energy from food is transferred to high energy compounds for quick and easy access.

97. ADP to ATP: Phosphorylation
ADP vs. ATP:
adenosine diphosphate (ADP):
2 phosphate groups (di = 2)
adenosine triphosphate (ATP):
3 phosphate groups (tri = 3)
Adding a phosphate group to ADP with a high-energy bound to form the high-energy compound ATP
ATPase:
the enzyme that catalyzes phophorylation

98. The Energy Molecule Chemical energy stored in phosphate bonds
Figure 2–24

99. A large organic molecule composed of the sugar ribose, nitrogenous bases, and phosphate groups is which kind of nucleic acid?
A. DNA
B. ATP
C. tRNA
D. RNA

100. What molecule is produced by the phosphorylation of ADP?
A. ATPase
B. ATP
C. Adenosine Diphosphate
D. Uridine Triphosphate

101. Compounds Important to Physiology
Table 2–8

102. SUMMARY
Atoms, molecules, and chemical bonds control cellular physiology
Metabolism and energy work within the cell
Importance of organic and inorganic nutrients and metabolites

103. SUMMARY Role of water and solubility in metabolism and cell structure
Chemistry of acids and bases, pH and buffers
Structure and function of carbohydrates, lipids, proteins, and nucleic acids
AnnMarie Armenti, MS SCCC BIO 130