2

Molecular Interactions
About this Chapter
0*Atoms, ions, and molecules 1*Types of chemical bonds 2*Biomolecules 3*Solutions, concentrations, and pH 4*Protein interactions

Atoms
5*Structure of an atom
6* Protons 7* Electrons 8* Neutrons

9*Nucleus 10* Electron orbitals or shells

Elements
11* 12* 13* 14* Essential Trace Atomic number Atomic mass

Isotopes
15* Isotopes vary in mass
Neutrons Radioisotopes Unstable nuclei Emit energy radiation Medical uses as tracers

16* 17* 18* 19* 20*

Ions
21* Ions are charged atoms
Cations Positively charged (+) Anions Negatively charged (-)

22* 23* 24* 25*

Atoms, Elements, Ions, and Isotopes

A map showing the relationship among atoms, elements, ions, and isotopes

Four Primary Roles of Electrons

26* 27* 28* 29* Covalent bonds Ions High-energy electrons Free radicals

Molecules and Compounds

30* 31* 32*

Bonds capture energy Bonds link atoms Molecules versus compounds

Molecules and Compounds

Shared electrons in the outer shells of atoms form covalent bonds

Types of Chemical Bonds

33* Covalent
Polar versus nonpolar

34*

35* 36* 37*

Ionic Hydrogen Van der Waals

Covalent and Ionic Bonds

38* Covalent bonds
Share a pair of electrons

39*

40*

Ionic bonds
Transfer an electron Opposite charges attract

41* 42*

Covalent and Ionic Bonds

Ions and ionic bonds

Covalent and Ionic Covalent and Ionic

Ionic Bonds and Ions Hydrogen and Van der Waals

43* Hydrogen bonds
Weak and partial Water surface tension

44* 45*

46*

Van der Waals forces

Weak and nonspecific

47*

Hydrogen and Van der Waals

Hydrogen bonds between water molecules

Hydrogen and Van der Waals Molecular Shape and Function

48* Molecular bonds
Covalent Weak

49* 50*

51* 52*

Chemical formula Functional groups

Molecular Shape and Function

Chemical structures and formulas of some biological molecules

Functional Groups
53* 54* Direct reactivity of a molecule Common examples in biosystems

Functional Groups Types of Biomolecules

55* 56* 57* 58* Carbohydrates Lipids Proteins Nucleotides and nucleic acids

Carbohydrates
59* Most abundant
Carbon Hydrogen Oxygen

60* 61* 62*

63*

Simple
Monosaccharides (glucose, ribose)

64*

65*

Complex
Polysaccharides (glycogen, starch)

66*

Carbohydrates Carbohydrates Carbohydrates Lipids

67* 68* Carbon and hydrogen (little oxygen) Structurally diverse

69* 70* 71* 72* 73* 74* 75*

Eicosanoids Steroids Phospholipids Triglycerides Glycerol Fatty acid chains Saturated and unsaturated

Lipids and Lipid-Related Molecules Lipids and Lipid-Related Molecules Lipids and Lipid-Related Molecules Lipids and Lipid-Related Molecules Lipids and Lipid-Related Molecules Proteins
76* Amino acids
Essential Amino group Acid group

77* 78* 79*

80*

Protein structure
Polypeptides Primary through quaternary

81* 82*

83*

Most versatile

Levels of Organization in Protein Molecules Levels of Organization in Protein Molecules Levels of Organization in Protein Molecules Levels of Organization in Protein Molecules Levels of Organization in Protein Molecules Levels of Organization in Protein Molecules Proteins
84* 85* Fibrous Globular

Combination Biomolecules
86* Lipoproteins
Blood transport molecules

87*

88*

Glycoproteins
Membrane structure

89*

90*

Glycolipids
Membrane receptors

91*

Nucleotides, DNA, and RNA

92* Composition
Base, sugar, and phosphate(s)

93*

94*

Transmit and store

Information (genetic code)

95*

96* 97*

Energy transfer molecules ATP, cAMP, NAD, and FAD

Nucleotides, DNA, and RNA Nucleotides, DNA, and RNA Aqueous Solutions
98* Aqueous
Water-based

99*

100* Solution
101* Solute dissolves in solvent

102* Solubility
103* Ease of dissolving

104* Hydrophobic 105* Hydrophilic

Aqueous Solubility
Sodium chloride dissolves in water

Concentrations
106* Amount of solute in a solution 107* Mole
108* 6.02 1023 units of substance

109* Molarity
110* One mole in one liter

111* Equivalents
112* Molarity multiplied by charge

Concentrations
113* Weight /volume
114* Grams solute/ml solvent

115* Volume/volume 116* Percent solution

Hydrogen Ion Concentration (pH)

117* Acid
118* Contributes H+ to solution

119* Base
120* Decreases H+ in solution

121* pH
122* - log [H+]

123* Buffer minimizes changes of pH

Hydrogen Ion Concentration (pH)

pH scale

Protein Interactions
124* Soluble and insoluble 125* Binding
126* Selectivity

127* 128*

Specificity Affinity

Selective Binding: Induced-Fit Model

The induced-fit model of protein-ligand binding

Factors that Affect Affinity

129* Isoforms 130* Activation
131* 132* Cofactors Lysis

Modulators Alter Binding or Activity Competitive Inhibition Allosteric Modulation Allosteric Modulation Physical Regulators
133* Temperature 134* pH 135* Concentration of protein 136* Concentration of ligand

Summary
137* Atoms in review 138* Four types of chemical bonds

139* Four kinds of biomolecules 140* Aqueous solutions and pH 141* Proteins in focus