Chapter 2 Molecular Interactions About this Chapter Chemistry

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

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 -2 b

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 -5 a

Hydrogen bonds and surface tension Figure 2 -5 b

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 -6 b

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

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

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

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, c. AMP, NAD, and FAD

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

Nucleotides, DNA, and RNA • Nucleotides are made of bases, sugars, and phosphate groups NUCLEOTIDES ATP ADP c. AMP NAD FAD Bases Sugar Phosphate groups Adenine Adenine + + + Ribose 2 Ribose + + + 3 2 1 2 2 = A, G, C, T = A, G, C, U + + Deoxyribose Ribose + + 1 per nucleotide = = = Other component + + Nicotinamide Riboflavin NUCLEIC ACIDS: DNA RNA Figure 2 -11 (2 of 2)

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

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

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

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 (p. H) • Acid • Contributes H+ to solution • Base • Decreases H+ in solution • p. H • - log [H+] • Buffer minimizes changes of p. H

Hydrogen Ion Concentration (p. H) 1 M Na. OH • p. H scale Chemical hair removers Household ammonia Soap solutions Baking soda Pancreatic secretions Compatible with human life Saliva Urine (4. 5– 7) Tomatoes, grapes Vinegar, cola Lemon juice Stomach acid Figure 2 -15

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

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

Physical Factors • Temperature • p. H • 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 p. H Proteins in focus