Chapter 2 Molecular Interactions

About this Chapter Chemistry Review Molecular Bonds and Shapes Biomolecules Solutions, Acids, Bases, and Buffers Protein interactions

Atoms Structure of an atom Nucleus Electron orbitals or shells Atom has three components Protons Electrons Neutrons

Elements Simplest type of matter Essential Trace Atomic number Atomic mass

Isotopes Isotopes have different numbers of neutrons Different atomic mass Radioisotopes Unstable and emit energy Alpha, beta, gamma emissions Medical uses as tracers

Ions Ions are charged atoms Cations Positively charged (+) Anions Negatively charged (–)

Ionic Bonds and Ions Table 2-1

Atoms, Elements, Ions, and Isotopes A map showing the relationship among atoms, elements, ions, and isotopes Figure 2-1 Helium loses a proton (and two neutrons) to become hydrogen Different element Isotope of the same element Ion of the same element An atom that gains or loses protons becomes a An atom that gains or loses neutrons becomes an An atom that gains or loses electrons becomes an loses an electron gains a neutron Hydrogen-1, H Hydrogen-2, or deuterium, 2 H, is an isotope of hydrogen. H + is a hydrogen ion. ATOMS ProtonsNeutronsElectrons consist of Helium, He

Four Primary Roles of Electrons Covalent bonds Ions High-energy electrons Free radicals Unpaired electron highly reactive Antioxidants

Molecules and Compounds Bonds capture energy Bonds link atoms Molecules versus compounds 2 or more linked atoms A compounds contain different kinds of atoms. H 2 O vs O 2 The forces holding atoms in a molecule are chemical bonds. Types of bonds: Ionic - exchange of electronics making ions Covalent - shared electrons Polar unequal sharing Hydrogen bonds - between molecules

Molecules and Compounds Shared electrons in the outer shells of atoms form covalent bonds Figure 2-2b

Types of Chemical Bonds Water is a polar molecule Figure 2-3

Types of Chemical Bonds Covalent bonds Polar versus nonpolar Ionic bonds Hydrogen bonds

Covalent and Ionic Bonds Covalent bonds Share a pair of electrons Ionic bonds Atoms gain or lose electrons Opposite charges attract Exchange of electrons

Covalent and Ionic Bonds Ions and ionic bonds Figure 2-4, step 1

Covalent and Ionic Figure 2-4, step 2

Covalent and Ionic Figure 2-4, step 3

Hydrogen and Van der Waals Hydrogen bonds Weak and partial Water surface tension Van der Waals forces Weak and nonspecific

Hydrogen bonds and Van der Waals Hydrogen bonds between water molecules Figure 2-5a

Hydrogen bonds and surface tension Figure 2-5b

Molecular Shape and Function Molecular bonds determine shape Shape influences function Chemical formula Atoms in a molecule (no relation is given) Functional groups Molecular groups that often move together and give unique functions

Molecular Shape and Function Different ways of drawing chemical structures and formulas of glucose Figure 2-6b

Functional Groups Combinations of atoms that occur frequently in biological molecules Move among molecules as a single group

Functional Groups Table 2-2

Types of Biomolecules Know 4 major biomolecule groups, functions, composition and examples. Monomer / Polymer Carbohydrates Lipids Proteins Nucleotides and nucleic acids

Carbohydrates (CH 2 O) n Most abundant Made of carbon, hydrogen, oxygen Simple Monosaccharides (glucose, ribose) Complex Polysaccharides (glycogen, starch)

Carbohydrates Figure 2-7 (1 of 3) Fructose Glucose (dextrose) Galactose* MONOSACCHARIDES * Notice that the only difference between glucose and galactose is the spatial arrangement of the hydroxyl groups.

Carbohydrates Figure 2-7 (2 of 3) Glucose Fructose + + GalactoseGlucose+ Sucrose (table sugar) Maltose Lactose DISACCHARIDES Polymers: X 100s or 1000s

Carbohydrates Figure 2-7 (3 of 3) Animals Plants Yeasts and bacteria POLYSACCHARIDES Chitin (invertebrates only) Glycogen Glucose molecules Cellulose Starch Dextran Glycogen

Lipids Carbon and hydrogen (little oxygen) Structurally diverse Triglycerides / Neutral Fats – energy storage Glycerol Fatty acid chains Saturated and unsaturated Phospholipids - membranes Steroids – membranes/hormones Eicosanoids Thromboxanes, leukotrienes and prostaglandins

Lipids and Lipid-Related Molecules Figure 2-8 (1 of 5)

Lipids and Lipid-Related Molecules Figure 2-8 (2 of 5)

Lipids and Lipid-Related Molecules Figure 2-8 (3 of 5)

Lipids and Lipid-Related Molecules Figure 2-8 (4 of 5)

Lipids and Lipid-Related Molecules Figure 2-8 (5 of 5)

Proteins 20 Amino acids Amino group Acid group Essential amino acids must be obtained Four levels of protein structure Primary through quaternary Peptides, polypeptides, oligopeptides Most versatile

Amino Acids Taurine?

Levels of Organization in Protein Molecules Figure 2-9 (1 of 5)

Levels of Organization in Protein Molecules Figure 2-9 (2 of 5)

Levels of Organization in Protein Molecules Figure 2-9 (3 of 5)

Levels of Organization in Protein Molecules Figure 2-9 (4 of 5)

Levels of Organization in Protein Molecules Figure 2-9 (5 of 5)

Proteins Globular protein structure Figure 2-10

Combination Biomolecules Lipoproteins Blood transport molecules Glycoproteins Cell membranes Glycolipids Cell membranes

Nucleotides, DNA, and RNA Composition Base, sugar, and phosphate Transmit and store information DNA, RNA Transmit and store energy ATP, cAMP, NAD, and FAD

Nucleotides, DNA, and RNA Figure 2-11 (1 of 2) consists of Purine Pyrimidine RiboseDeoxyribose Adenine (A) Guanine (G) Cytosine (C) Thymine (T) Uracil (U) NUCLEOTIDE Phosphates Sugar Nitrogenous base

Figure 2-11 (2 of 2) Nucleotides, DNA, and RNA Nucleotides are made of bases, sugars, and phosphate groups ATP ADP cAMP NAD DNA RNA = = = = = = Adenine A,G,C,T A,G,C,U 2 Ribose Ribose Deoxyribose per nucleotide Nicotinamide FAD = Adenine Ribose 2 Riboflavin NUCLEIC ACIDS: NUCLEOTIDESBasesSugarPhosphate groups Other component

Nucleotides, DNA, and RNA Figure 2-12a–b Adenine Thymine Guanine Cytosine Uracil Hydrogen bonds Guanine Adenine Cytosine Thymine KEY (a) Ribbon model of DNA (b) Complementary Base Pairs Guanine-Cytosine base pair Adenine-Thymine base pair

Nucleotides, DNA, and RNA Figure 2-12c Adenine Thymine Guanine Cytosine Uracil Hydrogen bonds KEY (c) Stylized ribbon model of DNA Hydrogen bonds Sugar-phosphate backbone

Nucleotides, DNA, and RNA Figure 2-12d Adenine Thymine Guanine Cytosine Uracil Hydrogen bonds KEY (d) Stylized ribbon model of RNA Bases Sugar-phosphate backbone

Aqueous Solutions Aqueous Water-based Solution Solute dissolves in solvent Solubility Ease of dissolving Hydrophobic Hydrophilic

Aqueous Solubility Sodium chloride dissolves in water Figure 2-14

Concentrations Amount of solute in a unit volume of solution Mass of solute before it dissolves Number of molecules or ions

Concentrations Mole 6.02  1023 units of substance Gram molecular mass Expressed in Daltons Molarity One mole in one liter Equivalents Molarity multiplied by charge

Concentrations Weight /volume Grams solute/ml solvent Volume/volume Percent solution

Hydrogen Ion Concentration (pH) Acid Contributes H + to solution Base Decreases H + in solution pH - log [H + ] Buffer minimizes changes of pH

Hydrogen Ion Concentration (pH) pH scale Figure 2-15 Stomach acid Lemon juice Vinegar, cola Tomatoes, grapes Urine (4.5–7) Pancreatic secretions Baking soda Soap solutions Compatible with human life Household ammonia Chemical hair removers 1 M NaOH Saliva

Protein Interactions Soluble and insoluble Soluble include Enzymes Membrane transporters Signal molecules Receptors Binding proteins Regulatory proteins Immunoglobulins

Protein Interactions Binding Noncovalent bonds with other molecules Proteins are selective about bonding Molecular complementarity Specificity Affinity

Selective Binding: Induced-Fit Model The induced-fit model of protein-ligand (L) binding Figure 2-16

Factors that Affect Protein Binding Isoforms Activation Cofactors Lysis Modulation

Factors that Affect Protein Binding Attachment of cofactors activates the protein Figure 2-18

Modulators Alter Binding or Activity Table 2-3

Competitive Inhibition Figure 2-19

Allosteric Modulation Figure 2-20 (1 of 2) Binding site ACTIVE PROTEIN Allosteric activator INACTIVE PROTEIN Modulator binds to protein away from binding site. Protein without modulator is inactive. ALLOSTERIC ACTIVATION Ligand

Allosteric Modulation Figure 2-20 (2 of 2) Protein without modulator is active. Modulator binds to protein away from binding site and inactivates the binding site. INACTIVE PROTEIN ALLOSTERIC INHIBITION Allosteric inhibitor Binding site ACTIVE PROTEIN Ligand

Physical Factors Temperature pH Concentration of protein Up-regulation Down-regulation Concentration of ligand Maximum reaction rate Saturation

Physical Factors Figure 2-21

Summary Atoms in review Four types of chemical bonds Four kinds of biomolecules Aqueous solutions and pH Proteins in focus