02 Lecture Presentation

© 2017 Education, Inc. A Chemical Connection to Biology Biology is the study of life Organisms and their environments are subject to basic laws of physics and chemistry “Somewhere in the transition from molecules to cells, we will cross the blurry boundary between nonlife and life.” (p. 28) Knowing the vocabulary in this chapter is critical for understanding the basic chemistry that underlies all life on Earth. Study guide for chapter 2 is available in Canvas files. © 2017 Education, Inc. Figure 2.1 formic acid is used by these wood ants to protect themselves against predators and microbial parasites Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds Organisms are composed of matter and matter is made up of elements Matter is anything that takes up space and has mass An element is a substance that cannot be broken down to other substances by chemical reactions A compound is a substance consisting of two or more elements in a fixed ratio A compound has characteristics different from those of its elements (it has emergent properties) © 2017 Education, Inc. Figure 2.2 Na Sodium Cl Chlorine NaCl Sodium chloride The emergent properties of a compound The Elements of Life About 20–25% of the 92 natural elements are required for life (essential elements) Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur Trace elements are required by an organism in only minute quantities (iron, iodine, copper, etc) © 2017 Education, Inc. Table 2.1 Case Study: Evolution of Tolerance to Toxic Elements Some elements can be toxic Some species can become adapted to environments containing toxic elements For example, some plant communities are adapted to serpentine soils © 2017 Education, Inc. Figure 2.3 A Tiburon Mariposa lily growing on serpentine soil. Concept 2.2: An element’s properties depend on the structure of its atoms Each element consists of unique atoms An atom is the smallest unit of matter that still retains the properties of an element Atoms are composed of subatomic particles Relevant subatomic particles include Neutrons (no electrical charge) Protons (positive charge) Electrons (negative charge) © 2017 Education, Inc. Neutrons and protons form the atomic nucleus Electrons form a “cloud” of negative charge around the nucleus Neutron mass and proton mass are almost identical and are measured in daltons Electrons have almost no mass and can be considered as energy since they do all the work of chemical reactions. © 2017 Education, Inc. Figure 2.4 Cloud of negative charge (2 electrons) Nucleus + + Electrons ? + + ? (a) (b) Simplified models of a helium (He) atom Atomic Number and Atomic Mass Atoms of the various elements differ in number of subatomic particles An element’s atomic number is the number of protons in its nucleus An element’s mass number is the sum of protons plus neutrons in the nucleus Atomic mass, the atom’s total mass, can be approximated by the mass number © 2017 Education, Inc. Isotopes All atoms of an element have the same number of protons but may differ in number of neutrons Isotopes are two atoms of an element that differ in number of neutrons Radioactive isotopes decay spontaneously, giving off particles and energy © 2017 Education, Inc. Radioactive Tracers Radioactive isotopes are often used as diagnostic tools in medicine Radioactive tracers can be used to track atoms through metabolism They can also be used in combination with sophisticated imaging instruments © 2017 Education, Inc. A PET scan using radioactive isotopes Radiometric Dating A “parent” isotope decays into its “daughter” isotope at a fixed rate, expressed as the half-life In radiometric dating, scientists measure the ratio of different isotopes and calculate how many half-lives have passed since the fossil or rock was formed Half-life values vary from seconds or days to billions of years © 2017 Education, Inc. The Energy Levels of Electrons Energy is the capacity to cause change Potential energy is the energy that matter has because of its location or structure The electrons of an atom differ in their amounts of potential energy An electron’s state of potential energy is called its energy level, or electron shell © 2017 Education, Inc. Figure 2.6 A ball bouncing down a flight of stairs can come to rest only on each step, not between steps. Third shell (highest energy level in this model) Second shell (higher energy level) Energy absorbed First shell (lowest energy level) Energy lost (b) Atomic nucleus Electron Distribution and Chemical Properties The chemical behavior of an atom is determined by the distribution of electrons in electron shells Valence electrons are those in the outermost shell, or valence shell © 2017 Education, Inc. Figure 2.7 Hydrogen 1 First shell Atomic mass 4.003 He 2 Atomic number Element symbol Electron distribution diagram Helium He Lithium Second shell Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon Sodium Third shell Magnesium Silicon Phosphorus Sulfur Chlorine Argon 2 Li 3 Be 4 B 5 C 6 N 7 O 8 F 9 Ne 10 Na 11 Mg 12 AI 13 SI 14 P 15 S 16 CI 17 Ar 18 H Aluminum The periodic table of the elements shows the electron distribution for each element Figure 2.7 Hydrogen 1 First shell Atomic mass 4.003 He 2 Atomic number Element symbol Electron distribution diagram Helium He Lithium Second shell Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon Sodium Third shell Magnesium Silicon Phosphorus Sulfur Chlorine Argon 2 Li 3 Be 4 B 5 C 6 N 7 O 8 F 9 Ne 10 Na 11 Mg 12 AI 13 SI 14 P 15 S 16 CI 17 Ar 18 H Aluminum The chemical behavior of an atom is mostly determined by the valence electrons Figure 2.7 Hydrogen 1 First shell Atomic mass 4.003 He 2 Atomic number Element symbol Electron distribution diagram Helium He Lithium Second shell Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon Sodium Third shell Magnesium Silicon Phosphorus Sulfur Chlorine Argon 2 Li 3 Be 4 B 5 C 6 N 7 O 8 F 9 Ne 10 Na 11 Mg 12 AI 13 SI 14 P 15 S 16 CI 17 Ar 18 H Aluminum Elements with a full valence shell are chemically inert Electron Orbitals An orbital is the three-dimensional space where an electron is found 90% of the time Each electron shell consists of a specific number of orbitals These orbitals give 3-dimensional shape to atoms and facilitate in chemical bonding. The chemical reactivity of an atom arises from the presence of unpaired electrons in one or more orbitals. © 2017 Education, Inc. Figure 2.8 First shell Second shell Neon, with two filled shells (10 electrons) First shell Second shell 1s orbital 2s orbital x z Three 2p orbitals y (a) Electron distribution diagram (b) Separate electron orbitals 1s, 2s, and 2p orbitals (c) Superimposed electron orbitals Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms These interactions usually result in atoms staying close together, held by attractions called chemical bonds © 2017 Education, Inc. Covalent Bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atom’s valence shell A molecule consists of two or more atoms held together by covalent bonds A single covalent bond, or single bond, is the sharing of one pair of valence electrons A double covalent bond, or double bond, is the sharing of two pairs of valence electrons © 2017 Education, Inc. Figure 2.9_3 Hydrogen atoms (2 H) + + + + + + Hydrogen molecule (H2) The notation used to represent atoms and bonding is called a structural formula For example, H—H This can be abbreviated further with a molecular formula For example, H2 © 2017 Education, Inc. Figure 2.10 Name and Molecular Formula (a) Hydrogen (H2) Electron Distribution Diagram Lewis Dot Structure and Structural Formula Space- Filling Model H H (b) Oxygen (O2) O O (c) Water (H2O) O H H (d) Methane (CH4) H H C H H Bonding capacity is called the atom’s valence Covalent bonds can form between atoms of the same element or atoms of different elements A compound is a combination of two or more different elements Atoms in a molecule attract electrons to varying degrees Electronegativity is an atom’s attraction for the electrons in a covalent bond The more electronegative an atom is, the more strongly it pulls shared electrons toward itself © 2017 Education, Inc. In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule © 2017 Education, Inc. ?? ?? O H H ?+ ?+ H2O Ionic Bonds Atoms sometimes strip electrons from their bonding partners An example is the transfer of an electron from sodium to chlorine After the transfer of an electron, both atoms have charges A charged atom (or molecule) is called an ion © 2017 Education, Inc. Figure 2.12_2 + ? Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion (a cation) Cl? Chloride ion (an anion) Sodium chloride (NaCl) Figure 2.12_2 + ? Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion (a cation) Cl? Chloride ion (an anion) Sodium chloride (NaCl) A cation is a positively charged ion An anion is a negatively charged ion An ionic bond is an attraction between an anion and a cation Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride (table salt), are often found in nature as crystals © 2017 Education, Inc. Weak Chemical Interactions Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules Many large biological molecules are held in their functional form/shape by weak bonds The reversibility of weak bonds can be an advantage © 2017 Education, Inc. Hydrogen Bonds A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms © 2017 Education, Inc. Figure 2.14 ?– Water (H2O) ?– ?+ ?+ ?– Hydrogen bond Ammonia (NH3) ?+ ?+ ?+ Van der Waals Interactions If electrons are not evenly distributed, they may accumulate by chance in one part of a molecule Van der Waals interactions are attractions between molecules that are close together as a result of these charges © 2017 Education, Inc. Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface Molecular Shape and Function A molecule’s size and shape are key to its function A molecule’s shape is determined by the positions of its atoms’ orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes © 2017 Education, Inc. Figure 2.15 Space-Filling Model Ball-and-Stick Model Hybrid-Orbital Model (with ball-and-stick model superimposed) Unbonded electron pairs H O H 104.5º H O H Water (H2O) H C H H C H H H H H Methane (CH4) (b) Molecular-shape models s orbital z x Three p orbitals Four hybrid orbitals y Tetrahedron (a) Hybridization of orbitals Figure 2.15b Space-Filling Model Ball-and-Stick Model Hybrid-Orbital Model (with ball-and-stick model superimposed) O H Water (H2O) H C H H Methane (CH4) (b) Molecular-shape models 104.5º H Unbonded electron pairs O H H H C H H H H Molecular shape determines how biological molecules recognize and respond to one another Opiates, such as morphine, and naturally produced endorphins have similar effects because their shapes are similar and they bind the same receptors in the brain © 2017 Education, Inc. Figure 2.16 Natural endorphin Carbon Hydrogen Nitrogen Sulfur Oxygen Morphine (a) Structures of endorphin and morphine Natural endorphin Morphine Brain cell Endorphin receptors (b) Binding to endorphin receptors Concept 2.4: Chemical reactions make and break chemical bonds Chemical reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are called reactants The final molecules of a chemical reaction are called products © 2017 Education, Inc. Figure 2.UN03 2 H2 Reactants O2 Chemical reaction 2 H2O Products Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO2 + 6 H2O ? C6H12O6 + 6 O2 © 2017 Education, Inc. Figure 2.UN04 Reactants Sunlight Products 6 O2 Oxygen 6 CO2 Carbon dioxide 6 H2O Water C6H12O6 Glucose Figure 2.17 Leaf Bubbles of O2 All chemical reactions are reversible: Products of the forward reaction become reactants for the reverse reaction The two opposite-headed arrows indicate that a reaction is reversible 3 H2 + N ? 2 NH3 © 2017 Education, Inc. Chemical equilibrium is reached when the forward and reverse reactions occur at the same rate At equilibrium the relative concentrations of reactants and products do not change