8/28/13 1 Chapter 2 Chemical Components of Cells Why is biological chemistry important? Understanding the structure and properties of major classes of biological molecules is essential to understanding cellular function at any level.8/28/13 2 Be Able To • Compare ionic bonds, covalent bonds, hydrogen bonds, hydrophobic interactions, and van der Waals attraction. • Explain why covalent bonds are critical to biological systems. • Describe the unique properties of water that make them particularly important to life. • Calculate the pH of a solution given a concentration of a strong acid or base. Calculate the concentration of H+ or OH- given a pH. • Calculate the amount of stock solution or dry powder needed to create a specific solution. • Identify and draw the common functional groups found in chemistry (review Panel 2-1). An#atom#consists#of#a#posi-vely#charged#nucleus#and#a#nega-vely#charged#electron#cloud#8/28/13 3 The#number#of#protons#in#an#atom#determines#its#atomic#number,#and#its#number#of#electrons#Types of Chemical Bonds • Strong – Covalent bonds – Ionic bonds • Weak – Hydrogen Bonds – Hydrophobic Interactions – Van der Waals Attractions8/28/13 4 Figure 2-6 Essential Cell Biology (© Garland Science 2010) Strong#Bonds#Strength of Different Chemical Bonds Why is the strength of ionic bonds greatly affected by water but covalent bonds are not?8/28/13 5 Nonpolar covalent bonds Water has polar covalent bonds Asymmetric charge distribution The electrical charge effects of water can partially shield charges between ions8/28/13 6 Hydrogen bonds Electrostatic interaction between a H held in a polar covalent bond and another atom (usually O or N) also held in polar covalent bond. See Panel 2-2 and 2-7 Proper-es#of#Water#• Water'bond'angle'and'polar'covalent'bonds'produces'dipolar'molecule'• Many'proper7es'of'water'depend'on'ability'of'water'molecules'to'form'hydrogen'bonds'with'other'(polar'or'ionic)'molecules'• Unique'proper7es'of'H2O'– High'boiling'point'– High'specific'heat''– Liquid'at'RT'– Lower'density'as'solid'(ice'floats)'– Surface'tension,'etc.'8/28/13 7 Other#types#of#hydrogen#bonds#Hydrogen#Bond#to#Polar#Substances#8/28/13 8 Different#covalent#bond#geometries#Hydrophobic Interactions “Water fearing” attraction between nonpolar molecules caused by repulsion from water. Where in a cell might this type of interaction be needed? See Panels 2-2 and 2-78/28/13 9 Hydrophobic#interac-ons#van der Waals Attractions • Weak interaction caused by transient electrical charges, dependent on the distance between atoms • In large numbers can be significant in the attraction between macromolecular surfaces See Panel 2-78/28/13 10 Ionization of Water Acids, Bases and Buffers The#usual#range#of#pH#values#encountered#is#between#0#and#14!##8/28/13 11 Quantities of atoms and molecules • Atoms and molecules are very small so a scale factor is generally used to describe quantities - Mole • One Mole is 6 x 1023 individuals (Avogadro’s number) • The mass of 1 mole of a substance is determined from its atomic or molecular weight Example: Carbon has an atomic weight of 12 1 mole of carbon is 12 g 12 g of carbon contains 6 x 1023 atoms See Fig 2-3 for review Quantities of atoms and molecules Molar Solutions A molar solution has a concentration of 1 mole of a substance in one liter: 1 mole/l = 1 M Example: The molecular weight of NaCl is 58 g/mole. How many grams of NaCl are needed to make 1 liter of a 1 M solution? How many grams for 1 liter of a 100 mM solution? See inside text cover for units You must be able to answer these types of questions8/28/13 12 Ionization of Water H20 ↔ H+ + OH- Kw = [H+][OH-] = 1 x 10-14 [H+] = [OH-] = 1 x 10-7 pH = -log [H+] = 7 Acid/Base • An acid is any molecule capable of releasing (donating) a hydrogen ion (proton). – Ex: Acetic acid (CH3COOH), HCl, H20 • A base is any molecule capable of accepting a hydrogen ion (proton). – R-NH2, NaOH, H208/28/13 13 What is the pH of a 0.1 M HCl solution? HCl → H+ + Cl- [H+] = 0.1 M pH - strong acids pH = -log [H+] pH = -log 0.1 pH = -log10-1 pH = (-(-1)) pH = 1 What is the pH of a 0.1 M solution of NaOH? NaOH → Na+ + OH- [OH-] = 0.1 M Kw = [H+][OH-] = 10-14 [H+] = 10-14/[OH-] [H+] = 10-14/0.1 [H+] = 10-14/10-1 [H+] = 10-13 pH = -log [H+] = -log 10-13 = -(-13) = 13 pH - strong bases8/28/13 14 Many of the acids and bases important in the cell are weak partial dissociation, reversible Carboxyl group (-COOH) Amino group (-NH2) acid conjugate base base conjugate acid Review of pH Is a solution of pH 4 more acidic or alkaline than a solution of pH 6? By how much (x-fold)? You must be able to answer these types of questions8/28/13 15 Buffers • A buffer is a solution that resists change in pH when a small amount of acid or base is added • Consists of a mixture of a weak acid and its conjugate base or a weak base and its conjugate acid • The pH range over which a specific buffer “functions” is defined by its equilibrium dissociation constant Are cells buffered? Review of chemical groups commonly found in biological molecules • Methyl -CH3 nonpolar hydrocarbon • Hydroxyl -OH alcohols • Carboxyl -COOH weak acid • Carbonyl C=O – Ketone – Aldehyde • Amino -NH2 weak base • Amide O=C-NH2 carboxyl + amine • Phosphate -PO3 ester and anhydrides • Sulfhydryl -SH forms disulfide bonds Review Panel 2-18/28/13 16 Text questions you should try: 2-3 2-4 2-5 2-6 2-18 Be Able To • Describe the building blocks of the four major classes of biological molecules. • Describe the role for each of the major classes of biological molecules in life. • Draw the condensation/hydrolysis reaction given two molecules (i.e. glucose or a fatty acid). • Draw the various structures of sugars, lipid molecules, amino acids and nucleotides identified throughout the lecture.8/28/13 17 Four Major Classes of Biological Molecules Macromolecules are abundant in cells8/28/13 18 • Sugars have the general formula (CH2O)n hence the name carbohydrate. Most sugars have 3-7 carbons, with 6 carbon sugars (hexoses) being especially important. We will focus on glucose. You must know this structure! Fig. 2-16A • Polysaccharides function as stores of