Chapter 2 pt 1. Atoms, Molecules, and Life. Gregory Ahearn. John Crocker. Including the lecture Materials of

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1 Chapter 2 pt 1 Atoms, Molecules, and Life Including the lecture Materials of Gregory Ahearn University of North Florida with amendments and additions by John Crocker Copyright 2009 Pearson Education, Inc..

2 Primary steps of the scientific method Feedback falsifiable Question Research Hypothesis M & M/Data Results does not support hypothesis; revise hypothesis or pose new one Results: Experiment or additional observation Results supports hypothesis; make additional predictions and test them

3 If a hypothesis is correct, when we test it, we can expect a particular outcome We try to disprove hypothesis. Control groups are tested along with experimental groups to provide a comparison of results

4 Snowberry fly mimicking a jumping spider Figure 1.3Cx

5 Case study: spider mimicry Pounce rate (% of trials in which spider jumped on fly) Control group (untreated flies) Experimental group (wing markings masked) Figure 1.3D

6 Biosphere Ecosystem -abiotic factors -all organisms Community Population Organism ORGAN SYSTEM LEVEL Nervous system ECOSYSTEM LEVEL Eucalyptus forest COMMUNITY LEVEL All organisms in eucalyptus forest POPULATION LEVEL Group of flying foxes ORGANISM LEVEL Flying fox Brain Spinal cord ORGAN LEVEL Brain Nerve TISSUE LEVEL Nervous tissue CELLULAR LEVEL Nerve cell MOLECULAR LEVEL Molecule of DNA Figure 1.1

7 Organisms are made up of: organ systems organs tissues cells molecules ORGAN SYSTEM LEVEL Nervous system ECOSYSTEM LEVEL Eucalyptus forest COMMUNITY LEVEL All organisms in eucalyptus forest POPULATION LEVEL Group of flying foxes ORGANISM LEVEL Flying fox Brain Spinal cord ORGAN LEVEL Brain Nerve TISSUE LEVEL Nervous tissue CELLULAR LEVEL Nerve cell MOLECULAR LEVEL Molecule of DNA Figure 1.1

8 Each level of organization builds on the one below it At each level, new properties emerge Biological function starts at the chemical level ATOMS AND MOLECULES

9 2.1 What Are Atoms? Elements: substances that cannot be broken down by ordinary chemical means (ex/ carbon) all atoms belong to one of 96 types of naturally occurring elements life requires about 25 of these elements

10 2.1 What Are Atoms? Atoms: basic structural unit of matter consist of charged particles protons (+) neutrons (0) electrons (-) smallest particle of an element each element has a unique number of protons (atomic number)

11 Isotopes - Atoms of the same element with different numbers of neutrons Radioactive isotopes spontaneously break apart forming different kinds of atoms releasing energy in the process. Example: radioactive uranium isotopes decay and form lead in the process

12 Atoms are electrically neutral because they have and equal number of positive protons and negative electrons Protons Neutrons Electrons Nucleus Helium atom

13 Electrons are arranged in shells Electrons orbit around atomic nuclei at specific distances called electron shells the outermost shell determines the chemical properties of an atom Outermost electron shell (can hold 8 electrons) Electron First electron shell (can hold 2 electrons) HYDROGEN (H) Atomic number = 1 CARBON (C) Atomic number = 6 NITROGEN (N) Atomic number = 7 OXYGEN (O) Atomic number = 8

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15 Electrons can move from electron shell to electron shell. Electrons move from an inner to an outer shell when absorbing energy. Electrons move from an outer shell to an inner shell when releasing energy. All life depends on this energy. energy 1 An electron absorbs energy The electron drops back into lower-energy shell, releasing energy as light + The energy boosts the electron to a higher-energy shell light

16 Energy Capture and Release Life depends on electrons capturing and releasing energy Electron shells correspond to energy levels Energy exciting an atom causes an electron jump from a lower- to higher-energy shell Later, the electron falls back into its original shell, releasing the energy

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18 2.2 How Do Atoms Form Molecules? Molecules: two or more atoms of one or more elements held together by interactions among their outermost electron shells Atoms interact with one another according to two basic principles: An inert atom will not react with other atoms when its outermost electron shell is completely full or empty. A reactive atom will react with other atoms when its outermost electron shell is only partially full.

19 Atoms Interact Atoms will react with other atoms if the outermost shell is partially full (such atoms considered reactive) Example: Oxygen, with 6 electrons in outermost shell (can hold 2 more electrons)

20 Atoms Interact Reactive atoms gain stability by electron interactions (chemical reactions) Electrons can be lost to empty the outermost shell Electrons can be gained to fill the outermost shell Electrons can be shared with another atom where both atoms have full outermost shells

21 Atoms Interact Hydrogen and oxygen atoms gain stability by interacting with each other Single electrons from each of two hydrogen molecules fill the outer shell of an oxygen atom

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23 Atoms combine with each other to fill outer electron shells (e.g. hydrogen and oxygen have unfilled outer electron shells, and thus, can combine to form the water molecule). The water molecule, with a filled outer electron shell, is more stable than either the hydrogen or oxygen atoms that gave rise to it. The results of losing, gaining, or sharing electrons are chemical bonds attractive forces that hold atoms together in molecules.

24 2.2 How Do Atoms Form Molecules? A molecule may be depicted in several ways. H H H H H C C C C O H H H H H (a) All bonds shown CH 3 CH 2 CH 2 CH 2 OH (b) Bonds within common groups omitted OH (c) Carbons and their attached hydrogens omitted (d) Overall shape depicted Fig. 2-4

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26 Types of bonds Ionic bonds: formed by passing an electron from one atom to another One partner becomes positive, the other negative, and they attract one another. Na + + Cl becomes NaCl (sodium chloride) Positively or negatively charged atoms are called ions. + cation - anion

27 Ions and Ionic Bonds Atoms that have lost electrons become positively charged ions (e.g. sodium: Na + ) Atoms that have gained electrons become negatively charged ions (e.g. chlorine: Cl - ) Oppositely charged ions are attracted to each other are bound into a molecule by ionic bonds

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29 Ions and Ionic Bonds Salt crystals are repeated, orderly arranged sodium and chloride ions

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32 Types of bonds (continued) Covalent bonds: bond between two atoms that share electrons in their outer electron shell For example, an H atom can become stable by sharing its electron with another H atom, forming H 2 gas.

33 Covalent Bonds Atoms with partially full outer electron shells can share electrons Two electrons (one from each atom) are shared in a covalent bond

34 Covalent Bonds Covalent bonds are found in H 2 (single bond), O 2 (double bond), N 2 (triple bond) and H 2 O Covalent bonds are stronger than ionic bonds but vary in their stability Most biological molecules contain covalent bonds

35 Covalent bonds produce either nonpolar or polar molecules. Nonpolar molecule: atoms in a molecule equally share electrons that spend equal time around each atom, producing a nonpolar covalent bond

36 Nonpolar covalent bonding in hydrogen Same charge on both nuclei + + (uncharged) Electrons spend equal time near each nucleus (a) Nonpolar covalent bonding in hydrogen Fig. 2-6a

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38 Polar Covalent Bonds Atoms within a molecule may have different nuclear charges Those atoms with greater positive nuclear charge pull more strongly on electrons in a covalent bond In diatomic molecules like H 2, both atoms exert the same pulling force on bond electrons: the covalent bond is nonpolar

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40 Polar Covalent Bonds In molecules where atoms of different elements are involved (H 2 O), the electrons are not always equally shared: these covalent bonds are polar

41 Polar Covalent Bonds A molecule with polar bonds may be polar overall H 2 O is a polar molecule The (slightly) positively charged pole is around each hydrogen The (slightly) negatively charged pole is around the oxygen

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43 Hydrogen Bonds Hydrogen bonds: weak electrical attraction between positive and negative parts of polar molecules Example: the negative charge of oxygen atoms in water molecules attract the positive charge of hydrogen atoms in other water molecules

44 Hydrogen Bonds Polar molecules like water have partially charged atoms at their ends Hydrogen bonds form when partial opposite charges in different molecules attract each other The partially positive hydrogens of one water molecule are attracted to the partially negative oxygen on another

45 Hydrogen Bonds Polar biological molecules can form hydrogen bonds with water, each other, or even within the same molecule Hydrogen bonds are rather weak but can collectively be quite strong

46 Hydrogen bonds H (+) O ( ) H (+) O ( ) H (+) H (+) hydrogen bonds Fig. 2-7

47 2.2 How Do Atoms Form Molecules?

48 Free Radicals Some cellular reactions produce free radicals Free radical: a molecule whose atoms have one or more unpaired electrons in their outer shells Free radicals are highly unstable and reactive Free radicals steal electrons, destroying other molecules Cell death can occur from free radical attack

49 Free Radicals Free radicals are involved in causing heart disease, Alzheimer s, cancer, and aging Antioxidants like vitamins C and E can render free radicals harmless

50 2.3 Why Is Water So Important To Life? Water interacts with many other molecules. Oxygen released by plants during photosynthesis comes from water. Water is used by animals to digest food. Water is produced in chemical reactions that produce proteins, fats, and sugars.

51 Many molecules dissolve easily in water. Water is an excellent solvent, capable of dissolving a wide range of substances because of its positive and negative poles. example NaCl dropped into H 2 O The positive end of H 2 O is attracted to Cl. The negative end of H 2 O is attracted to Na +. These attractions tend to pull apart the components of the original salt.

52 Water as a solvent Cl Na + H Na + Cl H O Cl Na + Fig. 2-8

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54 Water-insoluble molecules are hydrophobic Water molecules repel and drive together uncharged and nonpolar molecules like fats and oils The clumping of nonpolar molecules is called hydrophobic interaction

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56 Water Molecules Tend to Stick Together Surface tension: water tends to resist being broken Cohesion: water molecules stick together Fig. 2-9

57 Water Molecules Tend to Stick Together Hydrogen bonding between water molecules produces high cohesion Water cohesion explains how water molecules can form a chain in delivering moisture to the top of a tree

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59 Water Molecules Tend to Stick Together Cohesion of water molecules along a surface produces surface tension Fishing spiders and water striders rely on surface tension to move across the surface of ponds

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61 Water Molecules Tend to Stick Together Water molecules stick to polar or charged surfaces in the property called adhesion Adhesion helps water climb up the thin tubes of plants to the leaves

62 Acid, Basic, and Neutral Solutions Water can form ions. Water dissociates to become H + and OH. H 2 O OH - + H + Acid solutions have more H + (protons). Alkaline solutions have more OH (hydroxyl ions). A base is a substance that combines with H +, reducing its concentration. ph measures the relative amount of H + and OH in a solution.

63 A water molecule is ionized. ( ) (+) O O + H H H H water (H 2 O) hydroxide ion (OH ) hydrogen ion (H + ) Fig. 2-10

64 Acid, Basic, and Neutral Solutions Solutions where H + > OH - are acidic e.g. Hydrochloric acid ionizes in water: HCl H + + Cl - Lemon juice and vinegar are naturally produced acids

65 Acid, Basic, and Neutral Solutions Solutions where OH - > H + are basic e.g. Sodium hydroxide ionizes in water: NaOH Na + + OH - Baking soda, chlorine bleach, and ammonia are basic

66 Acid, Basic, and Neutral Solutions The degree of acidity of a solution is measured using the ph scale phs 0-6 are acidic (H + > OH - ) ph 7 is neutral (H + = OH - ) ph 8-14 is basic (OH - > H + )

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68 Buffers Maintain Constant ph A buffer is a compound that accepts or releases H + in response to ph change The bicarbonate buffer found in our bloodstream prevents ph change

69 Buffers Maintain Constant ph If the blood becomes too acidic, bicarbonate accepts (and absorbs) H + to make carbonic acid HCO H + H 2 CO 3 bicarbonate hydrogen ion carbonic acid

70 Buffers Maintain Constant ph If the blood becomes too basic, carbonic acid liberates hydrogen ions to combine with OH - to form water H 2 CO 3 + OH - HCO H 2 O carbonic acid hydroxide ion bicarbonate water

71 Water stabilizes temperature Temperature reflects the speed of molecular motion Water has a high specific heat so it heats up very slowly It requires 1 calorie of energy to raise the temperature of 1g of water 1 o C Because it heats up very slowly water moderates the effect of temperature change Very low or very high temperatures may damage enzymes or slow down important chemical reactions

72 Water Stabilizes Temperature Water requires a lot of energy to turn from liquid into a gas (heat of vaporization) Evaporating water uses up heat from its surroundings, cooling the nearby environment (as occurs during sweating) Because the human body is mostly water, a sunbather can absorb a lot of heat energy without sending her/his body temperature soaring

73 Water Stabilizes Temperature Water requires a lot of energy to be withdrawn in order to freeze (heat of fusion) Water freezes more slowly than other liquids

74 Water Forms an Unusual Solid: Ice Most substances become denser when they solidify from a liquid Water molecules spread apart slightly during the freezing process Because of this ice is less dense than liquid water

75 Water Forms an Unusual Solid: Ice Ice floats in liquid water Ponds and lakes freeze from the top down and never freeze completely to the bottom

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77 Frozen water floats (left) and frozen benzene sinks (right) Figure 2.13x2

78 - Lower water is protected by the surface layer of ice. Life can survive in cold water underneath ice. Spring thaw pushes nutrient-rich bottom water to surface

79 Like no other common substance on earth, water naturally exists in all three physical states: solid liquid gas Figure 2.10B

80 Figure 2.10Bx

81 Organic vs. Inorganic in Chemistry Organic refers to molecules containing a carbon skeleton Inorganic refers to carbon dioxide and all molecules without carbon