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CAMPBELL BIOLOGY Outline TENTH EDITION Reece • Urry • Cain • Wasserman • Minorsky • Jackson I. Why study Chemistry II. Atoms A. B. C. D. 2 The Chemical Context of Life Periodic Table Isotopes Electrons/orbitals Bonding III. Bonds A. B. C. D. E. F. G. Dr Burns Napa Valley College Covalent bonds Polarity Ionic bonds Hydrogen bonding Van der Waals Interactions Shape/Structure Chemical Rxns © 2014 Pearson Education, Inc. Why study Chemistry? Chemistry is the basis for studying much of biology Biology follows the rules of physics and chemistry. Understanding chemistry is key to understanding how biological systems work Estuaries and wetlands can detoxify water: Runoff from agricultural land may have high levels of some elements such as selenium. Plants can take up selenium and convert it to gas, removing it from the water. We can use these plants to remove selenium = bioremediation Definitions and the Basics Matter – any substance that has mass and takes up space Elements are substances that can not be broken down into simpler substances by ordinary chemical reactions. The smallest unit of an element is the atom. If it is divided it will loose its unique properties What will cross a membrane? How is energy transferred through biological systems? What is a protein? The Elements of Life About 20–25% of the 92 elements are essential to life 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 those required by an organism in minute quantities © 2011 Pearson Education, Inc. 1 Table 2.1 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 Serpentine Soil Serpentine Plant Community low calcium-to-magnesium ratio lack of essential nutrients such as nitrogen, potassium, and phosphorus high concentrations of nickel and chromium 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 Subatomic Particles Atoms are composed of subatomic particles Subatomic particles include Neutrons (no electrical charge) Protons (positive charge) Electrons (negative charge) In each neutral atom the # of electrons = the # of protons 2 Figure 2.5 Atoms Cloud of negative charge (2 electrons) Neutrons and protons form the atomic nucleus Electrons Nucleus Electrons form a cloud around the nucleus Neutron mass and proton mass are almost identical and are measured in daltons (or atomic mass units, amus) (a) Electrons are found in the nucleus 1. True 2. False 50% (b) Atomic Number Atoms of the various elements differ in number of subatomic particles 50% An element’s atomic number is the number of protons in its nucleus e u Tr lse Fa Atomic Mass An element’s mass number is the sum of protons plus neutrons in the nucleus, this is the number at the bottom of the periodic table entry. Atomic Mass Mass of a proton ≈1 dalton Mass of a neutron ≈ 1 dalton Mass of an electron ≈ 1/1800 dalton Atomic mass, the atom’s actual total mass, can be approximated by the mass number 3 Isotopes Radioactive Isotopes Isotopes are atoms of the same element that have different numbers of neutrons Every atom of an element has the same number of protons. So all carbon atoms have six protons Radioactive Isotopes In 1896, Henri Becquerel placed a rock on unexposed photographic plates inside a drawer. The rock contained uranium. The isotopes of uranium emit energy. After a few days the plate had an image of the rock. A co-worker, Marie Curie, named this radioactivity. Radioisotopes in Medicine Radioactive isotopes are unstable, and become more stable by emitting energy and particles In contrast, most isotopes are stable Radioactive isotopes are used to date fossils and in medicine Figure 2.7 PET scans (Positron-Emission Tomography) Patient is injected with a compound that is labeled with an unstable isotope Cancer cells are growing faster and take up more of the compound than normal cells Abnormal tissue takes up less of the compounds Periodic Table The periodic table is a chart of the elements arranged by atomic number Cancerous throat tissue 4 Figure 2.9 Fig. 2.6a Hydrogen 1H Atomic number 2 He 4.00 Mass number First shell Helium 2He Element symbol Electron distribution diagram Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Second shell Sodium 11Na Magnesium Aluminum 12Mg 13Al Third shell Figure 2.7a 2 Atomic number He 4.003 Element symbol Atomic mass Answer the following questions for beryllium The atomic number = the # of protons in an atom Atoms have equal numbers of protons and electrons. How many protons does beryllium (Be) have? 1. 2. 3. 4. 5. One Two Three Four Five 20% 1 20% 20% 2 3 20% 4 20% 5 5 How many electrons does beryllium (Be) have? 1. 2. 3. 4. 5. One Two Three Four Five 20% 20% 20% 2 3 20% How many neutrons does beryllium (Be) have? 1. 2. 3. 4. 5. 20% One Two Three Four Five 20% O 1 4 33% 33% 1 1. 2. 3. 4. 1. 2. 3. 4. 5. 31 32 46 47 16 20% 1 Copyright © 2009 Pearson Education, Inc. 20% 2 20% 3 electrons neutrons protons none of the above 20% 4 25% 1 3 What is the mass number of an ion with 15 electrons, 16 neutrons, and a +1 charge? 20% o Th 20% e re Fo ur 20% Fi ve Isotopes are atoms of the same element that differ in their number of … 33% 2 Tw 5 What is the charge of an atom containing 12 protons, 11 neutrons, and 12 electrons? 1. -1 2. 0 3. +1 ne 20% 25% 25% 2 3 25% 4 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 20% 5 © 2011 Pearson Education, Inc. 6 Figure 2.6 (a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons. Third shell (highest energy level in this model) Second shell (higher energy level) First shell (lowest energy level) Energy absorbed Energy lost Atomic nucleus (b) Shell Model of Electrons This is not a correct illustration of their location, it is used to illustrate energy states Electron Orbitals An orbital is the three-dimensional space where an electron is found 90% of the time Electrons can be visualized as residing in shells around the nucleus (but they don’t reside here). The first shell can have up to two electrons The second shell and third shells can have up to eight electrons The outer most shell is the valence shell with the highest energy The chemical behavior of an atom depends mostly on the number of valence electrons Chemical Bonds Chemical bonds are unions between electron structure from different atoms Molecules are when two or more atoms join together. They can be the same element (H2) or different elements (H2O) When different elements join together, the molecule is referred to as a compound molecule © 2011 Pearson Education, Inc. 7 Electrons and Bonding If the valence shell is full, then the atom is non-reactive, inert, and does not form chemical bonds. Incompletely filled outer orbital, then the atom is reactive and will form chemical bonds. How many bonds, and what type of bond it can form depends on how many unfilled spots in outer shell Covalent Bonds Covalent Bonding A covalent bond is the sharing of a pair of valence electrons by two atoms Each atom has an attractive force for the other atoms unshared electrons, but not enough to take it completely away There can be single, double or triple covalent bonds Figure 2.11-3 Hydrogen atoms (2 H) 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 A triple covalent bond, or triple bond, is the sharing of three pairs of valence electrons Hydrogen molecule (H2) Figure 2.12a Animation: Covalent Bonds Name and Molecular Formula Electron Distribution Diagram Lewis Dot Structure and Structural Formula SpaceFilling Model (a) Hydrogen (H2) 8 Figure 2.12b Figure 2.12c Name and Molecular Formula Electron Distribution Diagram Name and Molecular Formula SpaceFilling Model Lewis Dot Structure and Structural Formula (b) Oxygen (O2) Electron Distribution Diagram SpaceFilling Model Lewis Dot Structure and Structural Formula (c) Water (H2O) Figure 2.12d How many covalent bonds can an atom form? Name and Molecular Formula Electron Distribution Diagram Lewis Dot Structure and Structural Formula SpaceFilling Model Each atom wants their outer shell filled. Hydrogen only has one electron in its shell – wants two, so it can form one bond. Carbon has four electrons in outer shell, wants eight, so it can form four bonds. (d) Methane (CH4) How many bonds can carbon form? 1. 2. 3. 4. One Two Three Four 25% 1 25% 25% 2 3 25% 4 How many bonds can hydrogen form? 1. 2. 3. 4. One Two Three Four 25% 1 25% 25% 2 3 25% 4 9 How many bonds can nitrogen form? How many bonds can helium form? 1. 2. 3. 4. None One Two Three 25% 1 25% 25% 2 3 One Two Three Four 25% 1 25% 2 25% 25% 3 2 3 25% 4 Some atoms have a greater pull on shared electron than other atoms The measure of this pull is electronegativity When a molecule is made up of atoms with different electronegativities it is a polar molecule The greater the pull the more electronegative (remember that electrons are negative) 4 Figure 2.13 – Nonpolar bonds the atoms have same pull on the shared electrons (H2) 25% Electronegativity Covalent bonds can be polar or nonpolar 25% 1 25% Types of Covalent Bonds One Two Three Four 4 How many bonds can oxygen form? 1. 2. 3. 4. 1. 2. 3. 4. 25% Polar bonds – the atoms don’t equally share O + H H H2O + the electrons (H2O) 10 Tab 2.2 Polarity Con’t Polar Covalent Bonding occurs with strong electrophiles (electronegative): atoms with nuclei that have a strong pull on electrons. Common examples in biological molecules include: Water Oxygen Nitrogen Sulfur (less than oxygen or nitrogen) Alcohol H H H H O C H H H H S N O H CH3 CH3 Aldehyde Ketone O O H2 C H3C H2 C C C H2 CH3 H3C C C H2 H H C HC Hydrocarbons H2 C H3C H2 C C H2 HC H H2 C C H2 CH3 C H2 H CH H CH C H C H Polar Functional Groups Carboxyl Oxygen containing: Carboxyl = - COOH Hydroxyl (alcohol) = - OH Phosphates = -PO4 Carbonyl Ketone = - CO Aldehyde = - CHO Nitrogen containing: Amino (-NH2) Thiols - Sulfur containing compounds (-SH) Alcohol CH3CH2CH2OH Ketone Aldehyde Ether Hydrocarbons CH3-O-CH2CH3 CH3CH2CH3 11 Which molecule is the most polar? 1. 2. 3. 4. 5. Nonpolar compounds CH3-SH CH3-NH2 CH3-O-CH3 CH3-OH CH3-COOH Hydrocarbons – lots of carbons and hydrogens bonded together Copyright © 2009 Pearson Education, Inc. Terminology Ionic Bonds Ion = atom that has gained or lost electrons, It no longer has a balance between protons and electrons, it is positive or negative charge Ionic bond is an association between ions of opposite charge: cations (positive) and anions (negative) Hydrophilic (water-loving) – polar molecules that are attracted to water Hydrophobic (water-fearing) – nonpolar molecules that are pushed aside by water Figure 2.12-1 Figure 2.12-2 + - Na Cl Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na Sodium atom Cl Chlorine atom Na+ Sodium ion (a cation) ClChloride ion (an anion) Sodium chloride (NaCl) 12 Page 21 Animation: Ionic Bonds Animation: Ionic Bonds Right-click slide / select “Play” © 2011 Pearson Education, Inc. In the reaction between sodium and chloride, which is being oxidized 1. Sodium 2. Chloride 50% 50% Weak Chemical Bonds Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules Weak chemical bonds are also indispensable Many large biological molecules are held in their functional form by weak bonds The reversibility of weak bonds can be an advantage 1 2 Copyright © 2009 Pearson Education, Inc. 13 Hydrogen Bonds A hydrogen bond forms when a hydrogen Hydrogen Bonding Weak attraction between a slightly positive hydrogen atom and an electronegative atom such as oxygen, nitrogen, or less commonly sulfur. Individually weak, but many together can be strong. Determines shapes of many biological molecules including proteins and DNA 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 © 2011 Pearson Education, Inc. Fig. 2.11a Figure 2.14 - + Water (H2O) + - Hydrogen bond Ammonia (NH3) + + + Fig. 2.11b Which of the following statements is correct about the atoms in ammonia (NH3)? 1. The N will have a slight positive charge 2. The N will have a strong positive charge 3. The H will have a slight positive charge 4. The H will have a slight negative charge 25% 1 25% 25% 2 3 25% 4 14 Van der Waals Interactions If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge Van der Waals interactions are attractions between molecules that are close together as a result of these charges What type of chemical bond results from an unequal sharing of electrons between two atoms? 1. 2. 3. 4. Polar covalent Nonpolar covalent Ionic Van der Waals 25% 1 25% 25% 2 3 25% 4 © 2011 Pearson Education, Inc. Molecular Shape and Function Figure 2.17 s orbital z Three p orbitals Four hybrid orbitals x y A molecule’s shape is usually very important to its function Tetrahedron (a) Hybridization of orbitals Space-Filling Model Ball-and-Stick Model A molecule’s shape is determined by the positions of its atoms’ valence orbitals Hybrid-Orbital Model (with ball-and-stick model superimposed) Unbonded Electron pair Water (H2O) Methane (CH4) (b) Molecular-shape models © 2011 Pearson Education, Inc. Molecular Shape and Function Figure 2.18 Carbon Hydrogen Natural endorphin Nitrogen Sulfur Oxygen Morphine Biological molecules recognize and interact with each other with a specificity based on molecular shape Molecules with similar shapes can have similar biological effects (a) Structures of endorphin and morphine Natural endorphin Brain cell Morphine Endorphin receptors (b) Binding to endorphin receptors © 2011 Pearson Education, Inc. 15 Chemical reactions 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 Figure 2.UN02 2 H2 + O2 Reactants 2 H2O Reaction Products © 2011 Pearson Education, Inc. Figure 2.UN07 Which of the following molecules is drawn correctly? Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO2 + 6 H20 → C6H12O6 + 6 O2 © 2011 Pearson Education, Inc. Important Concepts Reading for next lecture: Chapter 3 Know the vocabulary in the lecture/chapter What are the particles of an atom, their location, charge, and mass? Be able to read a periodic table and determine how many protons, neutrons, and electrons are in a neutral atom for each element. Important Concepts Be able to determine how many bonds each element can form. Understand the shell model and valence shells, valence electrons and how they are related to chemical bonds What are the four major types of bonds discussed in lecture and be able to describe them Identify polar and nonpolar molecules What are isotopes and radioactive isotopes, what are their similarities and differences? 16 Important Concepts Be able to draw two molecules hydrogen bonding with each other How is a molecule’s shape important in its function, what determines the shape? 17