Lecture 2, Life and Chemistry: Small Molecules PDF

2 Life and Chemistry: Small Molecules 2 Objectives (ILOs) A1. Be familiar with the chemical vocabulary discussed in class A2. Know the basic parts of an Atom and its properties A3. Understand the relationship between ene...

2 Life and Chemistry: Small Molecules 2 Objectives (ILOs) A1. Be familiar with the chemical vocabulary discussed in class A2. Know the basic parts of an Atom and its properties A3. Understand the relationship between energy level and electron orbit A4. Be familiar with the kinds of chemical bonds formed between atoms. Understand what causes their formation. A5. Be familiar with the kinds of chemical bonds formed between molecules. Understand what causes their formation. A6. Be familiar with the properties of water A7. Understand the relationship of kinetic energy and heat A8. Understand the concept of pH and be able to calculate the pH of a solution A9. Understand what an isomer is and be able to apply your understanding A10. Be familiar with the various functional groups B1. Be able to explain the importance of Carbon 2-2 2 Life and Chemistry: Small Molecules Atoms: The Constituents of Matter Chemical Bonds: Linking Atoms Together Chemical Reactions: Atoms Change Partners Water: Structure and Properties Acids, Bases, and the pH Scale Properties of Molecules 2-3 2 Atoms: The Constituents of Matter All matter is composed of atoms; atom is the smallest chemical unit Atomic structure determines the behavior of an element Atoms usually consist of 3 subatomic particles ‣ Proton ‣ Neutron ‣ Electron Each element contains only one type of atom. Information on elements is arranged in logical order in a table called the periodic table. 2-4 2 Atoms: The Constituents of Matter Each element has a unique atomic number which is the number of protons found in an atom of the element. The mass number is the number of protons plus the number of neutrons. The mass number is used as the weight of the atom, in units called daltons. (proton and neutron = 1 Dalton, electrons = 0 Daltons) The atomic weight (or atomic mass) is the average mass numbers of a representative sample of atoms of that element (with all the isotopes in their normally occurring proportions, see slide # 8) Each element has a unique symbol: H is hydrogen, C is carbon, Na is sodium, and Fe is iron. 2-5 2 A Portion of the Periodic Table A Portion of the Periodic Table. Each element has a unique atomic number and is represented by a unique one- or two letter symbol. The mass numbers given here are the most common for each element. 2-6 2 The Structure of Atoms Found in Organisms The Atomic Structure of the First 18 Elements. The most abundant elements in organisms are highlighted in blue. 2-7 2 Atoms: The Constituents of Matter All atoms of an element have the same number of protons, but not necessarily the same number of neutrons. Atoms of the same element that have different atomic weights are called isotopes. An isotope is an atom with a greater number of neutrons than other atoms of the same element In these images from live people, a radioactively labeled sugar is used to detect differences between the brain Radioactive Isotopes: Atomic nuclei that activity of a healthy person and that of a person who are unstable may lose a proton (decay) and abuses methamphetamines. The more active a brain energy (radiation). region is, the more sugar it takes up. The healthy brain (left) shows more activity in the region involved in memory (the red area) than the drug abuser’s brain does. Applications of radioactive isotopes: dating of objects (e.g. 14C), diagnosing disease. 2-8 Isotopes Have Different Numbers of Neutrons 2 Atoms: The Constituents of Matter The region in which an electron travels is called the electron’s orbital (3D space). The orbitals constitute a series of electron shells, or energy levels, around the nucleus. Two electrons at most can occupy each orbital. 2-10 2 Atoms: The Constituents of Matter The first shell is the innermost shell and has just one orbital, called the s orbital. The s orbital fills first and its electrons have the lowest energy. The second shell is next closest to the nucleus and has one s and three p orbitals. The second shell can accommodate eight electrons, two per orbital. 2-11 Electron Orbitals Electron orbitals. Each orbital holds up to two electrons. x Y Z 1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. (a) First shell (b) Second shell (c) Neon, with two filled shells (maximum (maximum (10 electrons) 2 electrons) 8 electrons) 2 Atoms: The Constituents of Matter The outermost shell (the valence shell) of an atom determines how it reacts with other atoms. The electrons found in the valence shell are referred to as valence electrons. In some elements, the outermost electron shell is not full; not all orbitals in the valence shell have two electrons and may have at least one unpaired valence electron—meaning at least one unfilled valence shell orbital. The number of unpaired valence electrons varies among elements. Carbon, for example, has four valence electrons, all unpaired. Oxygen has six valence electrons; four are paired, two are not. The number of unpaired electrons found in an atom is called its valence. Carbon’s valence is four, oxygen’s is two. 2-13 2 Atoms: The octet rule Generally, if eight electrons are in the outer shell, the atom is stable and does not tend to react. Atoms which do not have eight electrons in the outermost shell will share, gain, or lose electrons to arrive at a stable state. The tendency of atoms to be stable when they have eight electrons in their outermost shells is called the rule of eight, or the octet rule. Hydrogen and phosphorus are exceptions to the octet rule. 2-14 Electron Shells Determine the Reactivity of Atoms Electron Shells Determine the Reactivity of Atoms 2 Chemical Bonds: Linking Atoms Together A molecule is two or more atoms bonded together. A chemical bond is an attraction force that links two atoms together. A covalent bond is formed by sharing of a pair of electrons between two atoms. In hydrogen molecules (H2), a pair of electrons share a common orbital and spend equal amounts of time around each of the two nuclei. The nuclei stay some distance from each other due to mutually repelling positive charges. 2-16 2 Chemical Bonds: Linking Atoms Together Covalent bonds are very strong. Each covalent bond has a predictable length, angle, and direction, which makes it possible to predict the three- dimensional structures of molecules. A double covalent bond occurs when atoms share two pairs of electrons; in triple covalent bonds atoms share three electron pairs. 2-17 2 Quantifying Molecules The molecular weight of a molecule is the sum of the masses of all the atoms in the molecule. One mole, or 6.022 ´ 1023 molecules, has a mass equal to the molecular weight expressed in grams. The concentration of a substance in a solution is typically expressed as molarity (M), which is the number of moles per liter. 2-18 2 Chemical Bonds: Linking Atoms Together Electrons are not always shared equally between covalently bonded atoms. The attractive force that an atom exerts on electrons is called electronegativity. When a molecule has nuclei with different electronegativities, an electron spends most of its time around the nucleus with the greater electronegativity. What is responsible for an atom’s electronegativity? - It’s a combination of two things: the number of protons in the nucleus and the distance between the nucleus and the valence shell; i.e. the atomic radius. 2-19 2 Chemical Bonds: Linking Atoms Together Unequal sharing of electrons causes a partial negative charge around the more electronegative atom, and a partial positive charge around the less electronegative atom, resulting in a polar covalent The Polar Covalent Bond in the Water Molecule bond. Nonpolar covalent bond in hydrogen molecule Molecules that have polar covalent bonds are called polar molecules. Polar covalent bonds in water molecule 2-20 2 Which of the following molecules would you predict to have the largest number of polar covalent bonds based on their molecular formulas? A. C2H6O (ethanol) B. C2H6 (ethane) C. C2H4O2 (acetic acid) D. C3H8O (propanol) 2-21 2 Chemical Bonds: Linking Atoms Together Hydrogen bonds may form within or between molecules with polar covalent bonds. The d– portion of one molecule has a weak attraction to the d+ portion of another molecule. Each of these attractions is called a hydrogen bond. Hydrogen bonds do not share electrons. Although hydrogen bonds are weak, they tend to be additive, and they are of profound biological importance. 2-22 2 Chemical Bonds: Linking Atoms Together Ionic bonds involve a complete transfer of one or more electrons. Ions are formed when an atom loses or gains electrons. Positively charged ions are called cations. Negatively charged ions are called anions. 2-23 2 Chemical Bonds: Linking Atoms Together Ionic bonds are formed by the electrical attraction between ions with opposite charges. Table salt has chloride and sodium ions, held together by ionic bonds. When salt is introduced into water, the partial charges of the water molecules can easily interfere with the ionic bonds. 2-24 2 Chemical Bonds: Linking Atoms Together Polar molecules tend to be hydrophilic (= water loving). Substances that are ionic or polar often dissolve in water due to hydrogen bonds. Nonpolar molecules are called hydrophobic (= water fearing) because they tend to aggregate with other nonpolar molecules. Nonpolar molecules are also attracted to each other via relatively weak attractions called van der Waal’s forces (changing “hot spots” of positive and negative charges due to the random non-symmetrical distribution of electrons in molecules) 2-25 2 Polar and nonpolar attractions Hydrophilic: (Polar) Molecules and Hydrophobic: (Nonpolar) Molecules Ions Dissolve Readily in Water Do Not Dissolve in Water 2-26 2 Chemical bonds and interactions 2-27 2 Chemical Reactions: Atoms Change Partners Chemical reactions occur when atoms combine or change partners. In a chemical reaction, reactants are converted to products. A chemical reaction can be Bonding Partners and Energy May Change in a Chemical Reaction written as an equation. The equation must balance because matter is neither created nor destroyed. 2-28 2 Chemical Reactions: Atoms Change Partners Changes in energy usually accompany chemical reactions. Stored energy, such as that in chemical bonds, is called potential energy and is available for future use. We can measure the potential energy of molecules and express it in units of heat called calories. A calorie is the amount of heat required to raise the temperature of one gram of pure water from 14.5°C to 15.5°C. 2-29 2 Water: Structure and Properties Water is the solvent of life. Living organisms are over 70 percent water by weight and many reactions take place in this watery environment. A solution is a substance (the solute) dissolved in a liquid (the solvent). The mole concept is fundamental to quantitative analysis. A mole is the amount of a substance in grams whose weight is equal to its molecular weight. One mole of any given compound contains approximately 6.022 x 1023 molecules of that compound (Avogadro’s number). 2-30 2 Water: Structure and Properties A 1 molar (1 M) solution is one mole of a compound dissolved in water to make one liter. Example: One mole of NaCl is the atomic weight of Na (23) plus the atomic weight of Cl (35.5), or 58.5, in grams. When 58.5 grams of NaCl are dissolved in water to make one liter, the solution is 1 molar. 2-31 2 Water: Structure and Properties Due to its bent shape, polarity, and ability to form hydrogen bonds, water has some unusual properties. Ice is held in a crystalline structure by the orientation of water molecules’ hydrogen bonds. Each molecule forms hydrogen bonds with four other molecules. These four hydrogen bonds increase the space the water molecules take up, so water expands as it freezes, and ice is less dense than liquid water. For these reasons, ice floats in liquid water. 2-32 2 Water: Structure and Properties Compared to other nonmetallic substances, ice requires a lot of heat to melt because hydrogen bonds must be broken. The opposite process, freezing, requires water to lose a great deal of heat. 2-33 2 Water: Structure and Properties A great deal of heat energy is required to change the temperature of liquid water because the hydrogen bonds must be broken. Specific heat is the number of calories needed to raise one gram of a substance 1oC. The specific heat of liquid water is 1 Calorie (≈ 4 Joules). Liquid water has a higher specific heat than most other small molecules in liquid form. 2-34 2 Specific Heat As molecules increase in overall polarity, and thus in their ability to form hydrogen bonds, it takes an extraordinarily large amount of energy to change their temperature. 2-35 2 A Closer Look at the Properties of Water Cohesion – binding between like molecules § Results in high surface tension Adhesion – binding between unlike molecules Water expands as it changes from a liquid to a solid. § This is why ice floats (slide 32)! Water has an extraordinarily large capacity for absorbing heat. § High specific heat § High heat of vaporization 2-36 2 Water: Structure and Properties Water has a cohesive strength because of hydrogen bonds. The cohesive strength of water molecules allows the transport of water from the roots to the tops of trees. Water has high surface tension, which means that the surface of liquid water is relatively difficult to puncture. 2-37 2 Electrostatic attractions between partial charges on water and opposite charges on ions; hydrogen bonds; water and other polar molecules. ice to float; freezing solid. lots of heat energy; break hydrogen bonds and change water to a gas. 2-38 2 Acids, Bases, and the pH Scale Some substances dissolve in water and release hydrogen ions (H+); these are called acids. Their release is called ionization. Other substances dissolve in water and release hydroxide ions (OH–); these are called bases. Acids donate H+; bases accept H+. 2-39 2 Acids, Bases, and the pH Scale Acids release H+ ions in Bases accept H+ in solution. solution. If the reaction is NaOH ionizes completely complete, it is a strong to Na+ and OH–. The OH– acid, such as HCl. absorbs H+ to form water. The carboxyl group It is a strong base. (—COOH) is common in The amino group (—NH2) biological compounds. It is an important part of functions as an acid many biological because compounds; it functions —COOH à as a weak base by —COO– + H+ accepting H+: —NH2 + H+ à 2-40 —(NH3)+ 2 Acids, Bases, and the pH Scale pH is the measure of hydrogen ion concentration. It is defined as the negative logarithm of the hydrogen ion concentration in moles per liter. pH = −log [H+] The pH scale indicates the strength of a solution of an acid or base. The scale values range from 1 through 14. A pH 7 means the concentration of hydrogen ions is 1 x 10–7 moles per liter of water. A change of 1 pH unit means a 10-fold change in H+ concentration. Note that: Greater H+ concentration – lower pH – more acidic 2-41 Lower H+ concentration – higher pH – more basic/alkaline 2 Acids, Bases, and the pH Scale A buffer is a mixture of a weak acid and its corresponding base. Because buffers can react with both added bases and acids, they make the overall solution resistant to pH change. Buffers illustrate the law of mass action: - Addition of reactants to one side of a reaction drives the reaction in the direction that uses that component. 2-42 2 Properties of Molecules Chemists use the characteristics of composition, structure, reactivity, and solubility to help classify molecules. Two other properties that influence the behavior of molecules are the presence of recognizable functional groups, and the existence of isomers of molecules. 2-43 2 Properties of Molecules Functional groups give specific properties to molecules. Carbonyl groups Functional groups are covalently bonded to organic molecules. Amino acids are biological molecules that contain both a carboxyl group and an amino group. 2-44 2 Isomers Isomers are molecules that have the same chemical formula but different arrangements of the atoms. 2-45 2 Isomers (formerly called geometric isomers) 2-46 2 Isomers (Chiral molecules) 2-47