1. Ch 2: Molecular Interactions
Or, Chemistry class in one lecture!
Key Concepts
Elements, Atoms, Isotopes etc.
Chemical formulas, Chemical bonds
Solutions, Concentrations, pH
Organic Chemistry / Biochemistry

2. Element = Building block of matter
Periodic Table of the Elements
In human: 11 major essential elements C, O, H, Na, Se, P, Mg, Mn, K, Ca, Fe = trace elements
Organic Chemistry = Chemistry of Carbon

4. Structure of Atoms (AKA elements)
Some Terminology:
Atomic Number
Atomic mass
Ion
Isotope

5. Atomic Mass
Usually, the number of neutrons in the nucleus of an atom is equal to the number of protons.
However, many chemical elements can exist in multiple forms, called isotopes, which differ in the number of neutrons they contain.
For example, the most abundant form of the carbon atom, 12C, contains 6 protons and 6 neutrons, and has an atomic number of 6 and an atomic weight of 12.
The radioactive carbon isotope 14C contains 6 protons and 8 neutrons, giving it an atomic number of 6 but an atomic weight of 14.

6. Isotopes = Atoms of an element that have different numbers of neutrons
Isotopes = Atoms of an element that have different numbers of neutrons. Same Atomic Number, variable Atomic Mass
Most common
Much rarer
Heavy water = ?

7. Some isotopes are unstable: Radioisotopes
3 types of radiation:
 radiation – protons and neutrons
Generally not dangerous to life unless inhaled or ingested
Commonly emitted from radioactive substances like uranium
Does not travel far

8. Some isotopes are unstable: Radioisotopes
 radiation - electrons
Relatively harmless
Medium penetrating power
Can mutate DNA if struck
Used to kill cancer cells

9. Nuclear Medicine: use of radioisotopes in
diagnosis & treatment of disease.
127I is “normal” iodine
131I has 4 extra neutrons
 and  radiation
Medical Imaging ? Treatment?

10. Some isotopes are unstable: Radioisotopes
-Radiation
High energy waves, not particles
Gamma Radiation can penetrate thick material
Since Gamma Radiation is more penetrating it can cause the most damage to the human body
Gamma knife
Used for benign or malignant tumors of the brain

11. Alpha radiation consists of helium-4 nucleus and is readily stopped by a sheet of paper. Beta radiation, consisting of electrons, is halted by an aluminium plate. Gamma radiation is eventually absorbed as it penetrates a dense material. Lead is good at absorbing gamma radiation, due to its density.

16. Atoms: the Subunits of Elements
The chemical properties of atoms can be described in terms of three subatomic particles—protons, neutrons, and electrons.
The protons and neutrons are confined to a very small volume at the center of an atom called the atomic nucleus.
The electrons revolve in orbitals at various distances from the nucleus.

17. The Chemistry of Life Elements = Atoms Nucleus Orbit Protons Neutrons
Electrons

18. Atomic Number
Each chemical element contains a specific number of protons, and it is this number that is known as the atomic number.
Example: hydrogen has an atomic number of 1, so it has a single proton.
Because an atom is electrically neutral, the atomic number is also equal to the number of electrons in the atom.

19. Atoms Atomic number Atoms must be neutral
The number of protons, usually also equals the number of electrons.
Atoms must be neutral
Atoms/molecules that are stable will not bond with other atoms/molecules.

22. Electron Bonding Outermost shell contains all pairs of electrons
Stable
Outermost shell contains at least one unpaired electron
Unstable
Lose, gain or share electrons to become stable
An atom is most stable when each electron is paired!

23. Chemical Bonds
Ionic: electrons pulled from one atom to another: Na+ and Cl-
Covalent: electrons shared equally
Hydrogen: weak attraction
-Causes surface tension in water.

24. Chemical Bonds Ions are often called electrolytes! Ions Ionic Bonds
More (or less) electrons than protons
Ionic Bonds
Anions
Negative
Cations
Positive
Ions are often called electrolytes!

25. Ions
If an atom gains or loses one or more electrons, it acquires a net electric charge and becomes an ion.
Hydrogen atoms and most mineral and trace element atoms readily form ions.
Ions that have a net positive charge are called cations.
Examples: Ca2+, Na+
Ions that have a net negative charge are called anions.
Example: Cl-
Because of their charge, ions are able to conduct electricity when dissolved in water; consequently, the ionic forms of mineral elements are collectively referred to as electrolytes.

26. Ionic Bonds
Give away or receive electrons to create ions and for each ion to become more stable
Ions of opposite charge bind with each other to form an ionic bond
An ionic bond typically includes a metal
NaCl

27. Ionic Bonding

28. Ionic Bonds
Ionic bonds tend to dissociate in water as each constituent ion is attractive to the partial charges of water molecules.

29. Important Ions in Physiology
cations
anions

30. Chemical Bonds
Covalent
Polar
Non-polar

31. Covalent Bonds
Strong bonds that occur when two atoms share electrons in order to become more stable

32. Covalent Bonds Non-polar Covalent Bonds Polar Covalent Bonds
If the electrons are shared equally between atoms
Polar Covalent Bonds
If electrons spend more time around one atom than the other
Molecules develop regions of partial positive and negative charges

33. Covalent Bonds

35. Hydrogen Bonds Link Adjacent Water Molecules

36. Chemical Bonds Hydrogen Bonds Surface tension
Attractive force between water molecules that causes water to form spherical droplets
Weak attractive force between hydrogen and oxygen, nitrogen or fluorine atoms
Quickly forms and quickly breaks

37. Reactions Types of Reactions A + B C AB A + B AB + C AC + B
Synthesis Reaction--Anabolic
A + B C
Decomposition Reaction--Catabolic
AB A + B
Exchange Reaction
AB + C AC + B

38. Chemical Reactions Reactants form Products A + B AB
Anabolic or Synthesis Reaction

40. Chemical Reactions
Decomposition Reaction
Catabolic
AB A + B

42. Acid Base Reactions Acids
The concentration Hydrogen ions free in solution
Acids increase the concentration of H+ in a solution.
Protons H+

43. Acid Base Reactions Bases Are proton acceptors
Bases decrease the concentration of H+ in a solution.
Bind with hydrogen ions
Hydroxyl ion = OH-
Bicarbonate ion = HCO3-

45. Buffers
Buffers resist abrupt and large swings in the pH of body fluids.
To resist large changes in pH, the body releases hydrogen ions when the pH rises and binds hydrogen ions with bicarbonate ions when the pH drops.
Blood pH = 7.35 – 7.45

46. Buffers
CO2 + H2O H2CO H++ HCO3-

47. End of Inorganic Chemistry

48. BIOMOLECULES
Carbohydrates
Fats
Proteins

49. Organic Compounds Carbohydrates
A group that includes things like table sugars and starches.
Includes Simple and Complex groups

50. Simple Carbohydrates Simple Monosaccharides Disaccharides Fructose
Glucose
Disaccharides
Sucrose
Lactose

51. Monosaccharides

52. Disaccharides

53. Glycogen: a Polysaccharide

54. Complex Carbohydrates
Polysaccharides are long branching chains of simple sugars, specifically glucose.
Starch is a storage carbohydrate in plants.
Glycogen is a storage carbohydrate in animals.
Liver and muscles

55. How the Body Uses Sugars
Glycogen exists in the body as a reservoir of available energy that is stored in the chemical bonds within individual glucose monomers.
Hydrolysis of glycogen, as occurs during periods of fasting, leads to release of the glucose monomers into the blood, thereby preventing blood glucose from decreasing to dangerously low levels.
Glucose is often called “blood sugar” because it is the major monosaccharide found in the blood.

56. Lipids
Lipids are molecules composed predominantly (but not exclusively) of hydrogen and carbon atoms.
These atoms are linked by nonpolar covalent bonds. Thus, lipids are nonpolar and have a very low solubility in water.
Lipids can be divided into four subclasses: fatty acids, triglycerides, phospholipids, and steroids.
Solid at room temp = fat;
Liquid at RT = oil

57. Triglycerides

58. polyunsaturated) fats are liquid at room temp.
Unsaturated (mono- &
polyunsaturated) fats
are liquid at room temp.
Trans fats have added hydrogen (hydrogenated) (p 29)
Triglycerides: 3 FA + Glycerol
Saturated Unsaturated Polyunsaturated

59. Trans Fats

60. Organic Compounds Lipids, Fats or Triglycerides
Composed of Glycerol backbone plus 3 fatty acid chains
Saturated Fats
Contains only single bonds between the carbons on the fatty acid chains
Solid at room temperature
Unsaturated Fats
Contains one or more double bonds between the carbons on the fatty acid chains
Semi-solid or liquid at room temperature
Mono, di- and polyunsaturated fats
Will only dissolve in other lipids and insoluble in water.
Like Dissolves in Like

61. Phospholipid

62. Phospholipids

63. Organic Compounds Phospholipids Modified triglycerides
Phosphorous head and two fatty acid tails
Amphipatic
Hydrophilic, as well as
Hydrophobic
Found only in human cell membrane as a bi-layer
Hydrophobic – Tails on the inside of the membrane
Hydrophilic – Heads on the outside of the membrane

64. Cholesterol

65. Steroids
Cholesterol decreases cell membrane permeability to small water-soluble molecules.

66. Steroids

67. Organic Compounds Steroids Parent compound is cholesterol.
Used for the production of steroid hormones.
Can dissolve in fatty substances.
Dissolves through cell membrane and nuclear membrane and attaches directly to DNA
Starts Transcription of proteins
Such as enzymes
Cholesterol can be produced through de-novo synthesis

68. Organic Compounds Proteins
composes 10 – 30% of cell mass and is the basic structural material of the body.
Some are structural.
Bones, hair, connective tissue
Some are functional.
Antibodies, enzymes, protein hormones

70. Amino Acids

71. Organic Compounds Amino acids. The Building Blocks of Protein
Composed of
an amine groups
a carboxyl group
a “R” or Functional group.
20 different types of amino acids
9 Essential
Must acquire these through the foods we eat
11 Non-essential
Can be produced through de-novo synthesis

72. Peptide Bond

73. Peptide Bonds
Most proteins contain from 1500 to 50,000 amino acids in the human body.

74. Primary Structure of a Polypeptide Chain74

75. Conformation
Interactions between side groups of each amino acid leads to bending, twisting, and folding of the chain into a more compact structure.
The final shape of a protein is known as its conformation. 75

76. Amino acid interactions76

77. Polypeptides: Conformations

78. Hemoglobin 78

79. Proteins
Hydrogen bonds form and break quickly and can thereby change the protein shape and its function

80. Protein Structure Globular Proteins Compact, spherical proteins
Have tertiary or quaternary structures
Also known as functional proteins
Antibodies
Hormones
Enzymes (catalysts)
Membrane Transporters
DNA Regulatory Proteins for transcription

81. Proteins Fibrous proteins are stable.
Globular proteins are very unstable.
Hydrogen bonds can form and break easily.
Hydrogen bonds can break when:
A PO4 group is added

83. Adenosine Triphosphate
The transfer of a high energy phosphate group to an enzyme causes a change in confirmation
The change in enzyme shape allows the enzyme to quickly catalyze the reaction

85. Protein Structure Change in shape of protein = Denatured
Change in conformation =
Change in configuration
Denatured
When globular proteins lose their shape they can’t perform their function any longer.
pH drops.
Temperature rises above normal levels.

86. Enzymes Enzymes are globular proteins that act as catalysts.
A catalyst speeds up a chemical reaction but it itself is not used up
Enzymes are recycled
The function of a globular protein depends on the arrangement of the atoms

87. Mechanism of Enzymes Three Basic Steps
The Enzyme binds with a substrate at its active site.
The Enzyme-Substrate Complex is rearranged to form a product.
The Enzyme releases the product and goes back to its original shape
The Enzyme can be used again to catalyze another reaction

88. Enzymes The job of an enzyme is to lower the activation energy
Some enzymes carry a helper of “cofactor” such as iron or copper.
Vitamins, especially B complex.

89. Feedback Inhibition of Biochemical Pathways

90. Activation Energy
Fig 4-3

91. Some more characteristics of enzymes:
Usually end in –ase
Inactive form: -ogen

92. Naming of Enzymes Kinase Phosphatase Peptidase Dehydrogenase
mostly suffix -ase
first part gives info on function
Kinase
Phosphatase
Peptidase
Dehydrogenase
examples

93. Protein Molecules Specificity
The ability of a protein to bind to a certain ligand or a group of related ligands
Some proteins are very specific about the ligands they bind, others bind to whole groups of molecules

94. Affinity
The degree to which a protein is attracted to a ligand is referred to as its Affinity.
High affinity proteins are more likely to bind a certain molecule than a low affinity protein