BIOLOGY. The Chemical Context of Life. Outline. Why study Chemistry? The Elements of Life. Definitions and the Basics

Transcription

1 2 The hemical ontext of Life Dr Burns Napa Valley ollege AMPBELL BIOLOGY TENT EDITION Reece Urry ain Wasserman Minorsky Jackson Outline I. Why study hemistry II. Atoms A. Periodic Table B. Isotopes. Electrons/orbitals D. Bonding III. Bonds A. ovalent bonds B. Polarity. Ionic bonds D. ydrogen bonding E. Van der Waals Interactions F. Shape/Structure G. hemical Rxns 2014 Pearson Education, Inc. Why study hemistry? hemistry is the basis for studying much of biology 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 Biology follows the rules of physics and chemistry. Understanding chemistry is key to understanding how biological systems work What will cross a membrane? ow is energy transferred through biological systems? What is a protein? 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 The Elements of Life About 20 25% of the 92 elements are essential to life arbon, 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 1

2 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 ommunity low calcium-to-magnesium ratio lack of essential nutrients such as nitrogen, potassium, and phosphorus high concentrations of nickel and chromium (more common in ultramafic rocks). 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

3 Atoms Figure 2.5 Neutrons and protons form the atomic nucleus loud of negative charge (2 electrons) Nucleus Electrons 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) (b) Electrons are found in the nucleus Atomic Number 1. True 2. False 50% 50% Atoms of the various elements differ in number of subatomic particles An element s atomic number is the number of protons in its nucleus True False Atomic Mass 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. 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

4 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, enri 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 urie, named this radioactivity. Radioactive Isotopes Radioactive isotopes are unstable, and become more stable by emitting energy and particles In contrast, most isotopes are stable Radioisotopes in Medicine PET scans (Positron-Emission Tomography) Patient is injected with a compound that is labeled with an unstable isotope ancer cells are growing faster and take up more of the compound than normal cells Abnormal tissue takes up less of the compounds Radioactive isotopes are used to date fossils and in medicine Figure 2.7 Periodic Table The periodic table is a chart of the elements arranged by atomic number ancerous throat tissue 4

5 Fig. 2.6a Figure 2.9 First shell Second shell ydrogen 1 Lithium 3Li Beryllium 4Be Boron 5B Mass number arbon 6 Nitrogen 7N 2 e 4.00 Atomic number Element symbol Oxygen 8O Electron distribution diagram Fluorine 9F elium 2e Neon 10Ne Third shell Sodium 11Na Magnesium 12Mg Aluminum 13Al Silicon 14Si Phosphorus 15P Sulfur 16S hlorine 17l Argon 18Ar Figure 2.7a 2 e Atomic mass Atomic number Element symbol The atomic number = the # of protons in an atom Atoms have equal numbers of protons and electrons. Answer the following questions for beryllium ow many protons does beryllium (Be) have? 1. One 2. Two 3. Three 4. Four 5. Five 20% 20% 20% 20% 20%

6 ow many electrons does beryllium (Be) have? ow many neutrons does beryllium (Be) have? 1. One 2. Two 3. Three 4. Four 5. Five 20% 20% 20% 20% 20% 1. One 2. Two 3. Three 4. Four 5. Five 20% 20% 20% 20% 20% One Two Three Four Five What is the charge of an atom containing 12 protons, 11 neutrons, and 12 electrons? Isotopes are atoms of the same element that differ in their number of % 33% 33% 1. electrons 2. neutrons 3. protons 4. none of the above 25% 25% 25% 25% What is the mass number of an ion with 15 electrons, 16 neutrons, and a +1 charge? % 20% 20% 20% 20% 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 opyright 2009 Pearson Education, Inc. 6

7 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) Energy absorbed First shell (lowest energy level) (b) Atomic nucleus Energy lost Shell Model of Electrons 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 This is not a correct illustration of their location, it is used to illustrate energy states 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 Electron Orbitals An orbital is the three-dimensional space where an electron is found 90% of the time hemical Bonds hemical bonds are unions between electron structure from different atoms Molecules are when two or more atoms join together. They can be the same element ( 2 ) or different elements ( 2 O) When different elements join together, the molecule is referred to as a compound molecule 7

8 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. ow many bonds, and what type of bond it can form depends on how many unfilled spots in outer shell ovalent 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 ovalent Bonds A single covalent bond, or single bond, is the sharing of one pair of valence electrons Figure ydrogen atoms (2 ) 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 ydrogen molecule ( 2 ) Animation: ovalent Bonds Figure 2.12a Name and Molecular Formula Electron Distribution Diagram Lewis Dot Structure and Structural Formula Space- Filling Model (a) ydrogen ( 2 ) 8

9 Figure 2.12b Figure 2.12c Name and Molecular Formula Electron Distribution Diagram Lewis Dot Structure and Structural Formula Space- Filling Model Name and Molecular Formula Electron Distribution Diagram Lewis Dot Structure and Structural Formula Space- Filling Model (b) Oxygen (O 2 ) (c) Water ( 2 O) Figure 2.12d ow many covalent bonds can an atom form? Name and Molecular Formula Electron Distribution Diagram Lewis Dot Structure and Structural Formula Space- Filling Model Each atom wants their outer shell filled. ydrogen only has one electron in its shell wants two, so it can form one bond. arbon has four electrons in outer shell, wants eight, so it can form four bonds. (d) Methane ( 4 ) ow many bonds can carbon form? ow many bonds can hydrogen form? 1. One 2. Two 3. Three 4. Four 25% 25% 25% 25% 1. One 2. Two 3. Three 4. Four 25% 25% 25% 25%

10 ow many bonds can helium form? ow many bonds can nitrogen form? 1. None 2. One 3. Two 4. Three 25% 25% 25% 25% 1. One 2. Two 3. Three 4. Four 25% 25% 25% 25% ow many bonds can oxygen form? Electronegativity 1. One 2. Two 3. Three 4. Four 25% 25% 25% 25% 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) Types of ovalent Bonds Figure 2.13 ovalent bonds can be polar or nonpolar Nonpolar bonds the atoms have same pull on the shared electrons ( 2 ) Polar bonds the atoms don t equally share the electrons ( 2 O) O O 10

11 Tab 2.2 Polarity on t Polar ovalent Bonding occurs with strong electrophiles (electronegative): atoms with nuclei that have a strong pull on electrons. ommon examples in biological molecules include: Oxygen Nitrogen Sulfur (less than oxygen or nitrogen) Water O Alcohol O N S 3 3 Ketone Aldehyde O O ydrocarbons Polar Functional Groups Oxygen containing: arboxyl = - OO ydroxyl (alcohol) = - O Phosphates = -PO 4 arbonyl Ketone = - O Aldehyde = - O Nitrogen containing: Amino (-N 2 ) Thiols - Sulfur containing compounds (-S) arboxyl Alcohol Ketone Aldehyde Ether ydrocarbons 322O 3-O

12 Which molecule is the most polar? Nonpolar compounds S N 2 ydrocarbons lots of carbons and hydrogens bonded together O O OO opyright 2009 Pearson Education, Inc. Terminology ydrophilic (water-loving) polar molecules that are attracted to water ydrophobic (water-fearing) nonpolar molecules that are pushed aside by water 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) Figure Figure Na l Na l Na l Na Sodium atom l hlorine atom Na Sodium atom l hlorine atom Na + Sodium ion (a cation) l - hloride ion (an anion) Sodium chloride (Nal) 12

13 Page 21 Animation: Ionic Bonds Animation: Ionic Bonds Right-click slide / select Play In the reaction between sodium and chloride, which is being oxidized 1. Sodium 2. hloride 50% 50% Weak hemical 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 1 2 The reversibility of weak bonds can be an advantage opyright 2009 Pearson Education, Inc. 13

14 ydrogen 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 ydrogen 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 Fig. 2.11a Figure Water ( 2 O) + - ydrogen bond Ammonia (N 3 ) Fig. 2.11b Nitrogen (N) is much more electronegative than hydrogen (). Which of the following statements is correct about the atoms in ammonia (N 3 )? 1. The N will have a slight positive charge 2. The N will have a strong positive charge 3. The will have a slight positive charge 4. The will have a slight negative charge 25% 25% 25% 25%

15 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. Polar covalent 2. Nonpolar covalent 3. Ionic 4. Van der Waals 25% 25% 25% 25% Molecular Shape and Function Figure 2.17 s orbital z Three p orbitals Four hybrid orbitals x A molecule s shape is usually very important to its function (a) ybridization of orbitals y Tetrahedron A molecule s shape is determined by the positions of its atoms valence orbitals Space-Filling Model Ball-and-Stick ybrid-orbital Model Model (with ball-and-stick model superimposed) Unbonded Electron pair Water ( 2O) Methane ( 4) (b) Molecular-shape models Molecular Shape and Function Figure 2.18 Natural endorphin arbon ydrogen Nitrogen Sulfur Oxygen Biological molecules recognize and interact with each other with a specificity based on molecular shape Morphine Molecules with similar shapes can have similar biological effects (a) Structures of endorphin and morphine Natural endorphin Morphine Brain cell Endorphin receptors (b) Binding to endorphin receptors 15

16 hemical reactions Figure 2.UN02 hemical 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 O O Reactants Reaction Products 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 O O O 2 Important oncepts Reading for next lecture: hapter 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 oncepts 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

17 Important oncepts Be able to draw two molecules hydrogen bonding with each other ow is a molecule s shape important in its function, what determines the shape? 17